The mother was incredibly, incredibly creepy...
Okay, so here is my basic interpretation of the movie, and my reasons for thinking the mother, at least as an adult, is a creep.
The mother went away to California and none of the family visits. Something in her childhood made her want to get away- and it could be both because of abuse she endured, but also because she was in an awkward situation.
Ryder is 17, which means if she got pregnant with him at age 17 (right before heading off too college) she would only be about 34 in the movie, but she looks at least 10 years older than that to me. Maybe they just got an old looking actress for the part, but both of Ryder's parents looked mid forties minimally, and possibly as old as early 50s. So I don't actually think Ryder was conceived in some incestuous union.
The mother looks older than the creepy uncle. Their ages are never stated, but my guess is that they would have been adolescents around the same time, with Ryder's mother being maybe a few years older than her younger brother. There is the part at the end where the uncle says that the chicken-fighting down at the water was the mother's idea and she instigated the games. It might have started out innocently enough, or the mother might be a predator who abused her younger brother in early adolescence, and because of sexist biases she was perceived to be the victim by their own mother.
When Molly comes out of the barn crying and bleeding, my interpretation was that the uncle, damaged by his sister in childhood and a predator now himself, had been molesting her and perhaps she had been healing when Ryder arrived. Then jostling around on his shoulders "chicken fighting" caused any pre-existing injury to re-open and she bled and panicked.
She was behaving in a sort of flirty way with Ryder right from the beginning, but especially in the barn. That sort of sexualized behavior is common in kids who have been molested.
What is interesting is that instead of making clear right at the beginning what is going on, and letting Ryder explain, the mother shuts him down and tries to hush him up. He is confused, hurt and angry and takes off to the abandoned shed, and he is asked by the mother to spend the night out in the shed, even though he is innocent. I believe the mother said something like "let them get a chance to get comfortable with you again" as if just turning a blind eye to a problem resolves it.
Then the mother comes to Ryder when he is sleeping and gives him the blanket, but also leans close to him to kiss him. This scene I found very creepy- she behaved much like my own mother when I was growing up, a complete disregard for his personal space and boundaries. There is growing suspicion that Ryder is a child molester and yet he is not allowed to speak his peace, because the mother is afraid of what? Being embarrassed? Ryder clearly believes that if he tells his relatives he is gay they will think him incapable of molesting Molly, because being gay would make him completely uninterested in girls. Or, that seems to be how he thinks that news will be taken by "stupid rednecks". Yet his mother shuts him down. Then she snuggles down to him and pulls out the sleeping bag right next to her son in the dark, even though he is clearly uncomfortable and he forcefully has to tell her "I don't want you here."
My interpretation was that the mother was predatory towards the uncle, who then became enraged at being unfairly blamed but also grew up to molest his own daughter. When Ryder arrives, the uncle sees a way to get back at the mother for her abuse of him and letting him take the blame, by setting Ryder up,. The mother does not want Ryder to speak out or clear the air because she is afraid that any detailed conversation will lead to her younger brother outing her. When the comments are written on the car, her main priority is erasing the proof and "burying" the evidence, not finding out who did it or confronting anybody. She behaves secretively and in a creepy fashion right from the beginning, because she is guilty and knows it.
When Ryder is invited over to the uncle's house, I got the feeling that the uncle was grilling Ryder about him being a "heartbreaker" to see if he was gay or not, because he suspected he was and was fishing for information about his sister, who he had resented all his life. Any "dirt" on her (and by extension, her son) would give him a sense of power over her... something to use against her (since she obviously cares more about maintaining appearances than in clearing her falsely accused son or helping him to clear his name and set the record straight).
I think at first the uncle was angry at Ryder and attacked him because he was his sister's son, but later on his feelings became mixed and he also somewhat identified with Ryder and his confusion, hence the mixed messages and wanting Ryder to feel "comfortable" in his house (even though Ryder clearly wasn't). Not inviting Ryder's parents over... upon reflection, I see it as both a way to manipulate Ryder but also because the uncle was molested by Ryder's mother and doesn't want to be near her. Even the gun scene can be interpreted in a mixed way- both as an unspoken threat to Ryder and by extension his mother (as Ryder might be expected to tell the mother and so the threat would therefore by passed onto the mother, who abused the uncle) but also because the uncle DID identify with Ryder, thought he might be a victim of his sister's perversion and on some level wanted his teenage nephew to be able to protect himself. The uncle had definite mixed feelings towards Ryder- and I think the anger was because Ryder was his nephew and the son of the woman who had molested him and then blamed him for it, but also because the uncle identifies with Ryder and on some level wants him to be safe.
The uncle and aunt also sort of pressure Ryder into singing, and he performs for them even though he clearly feels uneasy and confused. Again, this is another sign to me that he feels unable to say no for himself and set clear boundaries. An adult pressures him and he immediately gives in, whether it be letting the creepy aunt lady feel his short shorts, or sleeping in the shed even though he is innocent, keeping his mouth shut when he wants to tell his side of what happened publicly and is prevented from doing it, going into the little girl Molly's room because he feels he must, singing even though he is clearly uncomfortable... repeatedly, he lets others stomp on his personal boundaries instead of saying "no, I'd rather not." Kids who are abused often have trouble maintaining their personal boundaries, speaking up or sticking up for themselves. The song Ryder sings them is full of blatant sexual references, which most teenage boys would be embarrassed to say in front of adult relatives, yet he seems desensitized to the references. If his mother was abusing him (as I believed she was) then she might very well have spoken to him in a sexualized manner (at least in private) and so speaking to other adult relatives about sexual acts would be something Ryder would have been desensitized to through abuse.
There is also the bit right after Ryder runs away in anger where the twin boys come up in the truck and ask Ryder if he is "hiding" with mocking expressions on their faces. My sense was that the uncle has been implying certain things about his sister and trying to poison the rest of the family against her and her son. He says no (he isn't hiding) and the boys don't seem entirely convinced. If Ryder's uncle was spreading gossip about the mother being abusive and insinuating it (without actually coming out and saying it) then it might be reasonable to expect that the extended family might think Ryder himself to be one of her victim's. Hiding is prey behavior, not predator behavior.
There is also the bit with the blind woman at the beginning, coming up to Ryder and asking to feel his shorts, because they are apparently the shortest shorts the grandmother has ever seen (even if that was the case, why would you have to feel them physically? Another breach of personal boundaries, to which Ryder seems stunned and unable to resist, and stands there blankly while she feels up his leg). How completely inappropriate to start feeling up the leg of a 17 year old nephew to measure the length of his shorts. She then smiles creepily before waddling off. Was this a nod to the fact that part of the "family secret" might include sexual abuse on a more pervasive scale?
Also, I might have watched too many Stanley Kubrick movies, but Ryder's short-shorts were bright red, and at least with Kubrick, he used red to denote danger. Might it be a nod to Ryder having been sexually abused by his mother? If Ryder was molested by his mother, it might also explain why he believes himself to be gay. A boy sexually abused by his own mother might understandably be turned off girls, and yet he is forbidden from even expressing the truth about this fundamental aspect of himself when he feels it will help clear his name against unspoken but obvious molestation allegations.
At the end of the movie, Ryder's father turns on the radio for some music to break the awkward silence. The song that comes on (if I am not mistaken) is David Bowie's "heroes". It is worth noting these lyrics from that song, which seem especially creepy in light of the themes of this movie:
"And you, you can be mean
And I, I'll drink all the time
'Cause we're lovers, and that is a fact
Yes we're lovers, and that is that"
The father, also, at the end, keeps looking in the rear-view mirror at his son, repeatedly, with a rather concerned, haunted look on his face. I think he was haunted by the sudden realization that his son might be an abuse victim, more than simply wondering about the events of the last few days. I also noted a few times in this movie where Ryder is confused and sort of blanks out and stares off into space, blinking sort of robotically, almost if in a dissociative state. At the end of the movie when they are driving home he has the same creepy, unblinking look on his face but with a hint of a strange smile on it.
Here is a screenshot from that scene... you see the father concernedly looking at his son, the mother looking at the father teary-eyed and Ryder starring off into space with a rather unsettling smile, with his hands clasped together like an elementary school student. http://thefilmexperience.net/storage/Road%20Trip.jpg?__SQUARESPACE_CACHEVERSION=1458247813267
There are a few ways to interpret the scene above. One is the mother is crying because the trip has brought back unpleasant memories and her son is spaced out from the stress of the last few days and the father is concerned about his son's experiences, but you can also look at the photo above and see a woman who is guilty of abusing both her younger brother and her son, who is desperately afraid the truth will come out and is afraid that her husband is cluing in and is afraid her marriage might be in a downward spiral, and the boy in the backseat who is her victim, who attempted to speak out and get help and was thwarted repeatedly from doing it, dissociating from the stress. Run both scenarios through your head, look at the above picture, and tell me which one seems more likely given all the details of this film.
"We all go a little mad sometimes." - Norman Bates