paul is the father
here are a few indicators that paul is the father (some are recycled from what others have said). most of it is communicated through innuendo and symbolism (sorry if this is all muddled, but i'm really tired):
1) the rapport between rachel and paul during the interview in the beginning--they're practically flirting, although rachel doesn't seem to even know that's what she's doing. these sorts of interviews are conducted on a regular basis in the mormon church, and you can tell by rachel's reaction to mr. will that he had never been present at one of her interviews before, nor had the tape recorder. that means that rachel and paul have spent a lot of time alone together behind closed doors. i think rachel, being young and naive, was eager to please paul and be obedient to him, and that paul took sexual advantage of [read: raped] her. i think she didn't realize at first that what was happening was wrong and she was in denial about it resulting in pregnancy, but the reality hit her eventually.
2) she lost her nightgown. i actually think this is a symbolic thing, not an indication that she lost it during a romp with her fake father (although maybe that is what happened). i think it sort of stands for sexual purity lost.
3) she appears to be sexually experienced--she isn't shy about hanging out in her underwear, rolling around on the floor in a nightie that's way too small, kissing, or being seen naked in the shower--even though she grew up in a highly modest culture. granted, she's a bold, candid girl, but that kiss with johnny wasn't her first. but it doesn't seem like she associates sex with passion/love quite yet, because she's still so young and also because her first sexual experiences didn't come from her desire to be intimate with someone but to do god's will according to what her fake father told her it was. in other words, she's both "pure" and oddly jaded at the same time.
4) when she cries about clyde not believing she conceived the child through a miracle, it doesn't seem like it's actually because he doesn't believe her. it seems more like it's because she doesn't believe herself, and she knows she's lying.
5) she "confesses" to mr. will while she's visiting him in juvy. that's why he's so quiet and seems to sulk through the rest of the movie. his heart is broken. wouldn't yours be if you found out your father was raping your sister? you'd feel betrayed and really horrible for your sister's sake. this is why he later hits paul with the car door, and i agree with someone else who said it's why he chooses to stay--to protect his other sisters from paul.
6) also as someone else said, i think when clyde is sitting in the convertible alone is when he's processing the truth after rachel has just told him.
7) the way the camera work is done during rachel's speeches about her pregnancy and wondering who the father is--during certain moments, the camera follows paul and even lingers on his crotch. the camera also lingers on rachel's youngest sibling, who is still just a baby, kind of hinting that the baby and rachel's unborn child share the same father.
8) ... the fact that she finds her real father when she's looking for her baby's father--but actually she kind of DOES find her baby's father. it's kind of a switcheroo, where, in finding her own father and mistaking him for her baby's father, she actually is confronted with the reality that her fake father is her baby's father. does that make sense? she has, of course, known this all along, but this is the moment when she decides to go to juvy and tell her brother the secret.
9) rachel calls her child a child of god and says that she knows she did everything right, according to god's will. i think on one hand, i think it's an ironic statement and she's talking about being forced to have sex and how she was told that it was god's will. but i think on the other hand, she's also establishing that she did nothing wrong and will never blame herself or her baby for what her stepfather i did. i have mixed feelings about this, because i think incest survivors who end up pregnant have every right to get an abortion, and that it's in no way making the child pay for the sins of the father or whatever crap christian people say when they try to justify forcing rape victims to carry pregnancies to term. however, i like the fact that rachel never feels guilty or lets anyone make her believe she's in the wrong for what happened.
anyway, i think the people who made the film chose not to be explicit about who the father of rachel's child is because they wanted to preserve some of the innocence and magic that we feel through rachel, as well as her confusion and even the pain and frustration she feels at being confused about what's happening to her.
also, this film seems to me to be subtly about the hypocrisy of fundamentalist mormons (and of the mormon church, christianity, and adults in general) when it comes to sexuality. rachel was taught to remain "chaste" but her ignorance and her eagerness to honor her stepfather were used against her. these adults are sexually repressed and teach their children to be repressed too, but then they act out in ways that are harmful to themselves and their children.
anyway, that's my 2 cents. maybe i'm wrong, but yeah...