I liked the ending, but I saw some holes in it... (Spoilers)
I definitly liked that the film makers and the studio had the guts to stick with such an ending. The movie shows how the masses can be manipulated into believing whatever they are spoonfed as long as it keeps them calm and they don't have to think. I definitley respect the movie and its ending for what it had to say and for going against the Hollywood norm respectively.
But I do have a cople of quibs with Arlington Road.
First of all, it's strange that terrorists who simply seem to be motivated to wreak anarchy against the establishment would like to keep their involvement secret, especially religious ones like Lang is shown to be. It seems that such an organzation would like to take credit for their deeds. Blowing up the FBI building was the goal itself. They did it for the sake of sticking it to the man, not to achieve a particular goal that they would like to keep secret. Pinning the blame on a patsy is not what terroriists do because they terrorize to send a message. Cover-ups like the on in this movie are common in political and economic circles - when somebody needs to be taken out but his assasination shouldn't be linked with anybody's interests. For instance political assasinations. It does seem suspicious that a lone madman would decide to kill a politician for instance just because he's crazy. Why? because a lone madman would hardly be able to pull off something so sophisticated and would more likely just go on a random rampage. It's not exactly the same with Arlington Road because the patsies are shown as seeking revenge for something particular after having snapped unlike Lee Harvey Oswald for instance. But I still think transfering such a set-up to a terrorist context is a bad choice.
Check out The Parallax View if you haven't. It's about a secret (and probably governmental) agency that recruits mentally unstable young men and makes them assasins for political gains and thanks to their histories of being deranged, the killings are just ruled off as crimes of madness. But I prefer Arlington Road as a film because it really kept me engaged unlike Parallax that had something very important to say but said in a very dull manner. Arlington is also more memorable because you don't expect the twist, whereas the fate of the protagonist in Parallax (which is similar to that of Michael) was not a shock for me.
My second quib with Arlington Road is just how the bombing was pinned on Michael. It makes for a very nice twist and promotes the message of how people can be manipulated, but I don't see how it could be pulled off. The news report said that investigators had no idea what floor the explosion originated from. All the people that saw Michael with the bomb in his trunk were clearly blown up with him. That leaves only the security guards at the gate if we can assume they survived. They may have just said that they saw a guy in a frenzy with a beat up car jumping into the garage while rambling about a bomb. Assuming that it was he who did the bombing is the easiest possible explanstion and that is actually the point of the movie - that the authorities would be quick to use it to calm the masses. That sill doesn't explain how exactly they would know it was Michael Farraday. I didn't noptice him identifying himself or anything while he was at the gate. Maybe we can assume they wrote down his license number or something but I still think it's a plot hole.