Most religious fundamentalists in the US are uneducated and ignorant. They live in very small worlds and are so afraid of going to hell that they aren't willing to question anything they are told or to go out and meet people who are gay, trans, etc. to find out if those people really are evil.
As for hate crimes, I think they stem from both that ignorance and fear that if they don't react that way, they'll be seen as gay, etc.
For a little insight (in terms of interviews and observation), I'd recommend watching "Jesus Camp", "Friend of God: A Road Trip with Andrea Pelosi", and "Fall From Grace," which is about Fred Phelps and the Westboro Baptist Church in Topeka, Kansas (although in the Phelps' family case, I think it's just insanity). "Jesus Camp", in particular, gives some insight into what it is to be an evangelical Christian. Also, "Religulous" (film by Bill Maher) has an interesting scene in a truck stop chapel that might give some insight as well (although, on a whole, I didn't like that film as well because it is so one sided...I think it could have been a lot better).