I'm very sorry to learn he has had such a horrible thing happen. It does happen more often than most realize particularly with boys. It's a double blow for them since not only was their trust & bodies violated, but it also has the homosexual element to it which adds yet another level of anguish & shame which hetersexual rape victims do not have to face.
The fact that he was molested by someone from his church has caused him to feel God didn't protect him as he deserved to be but also now has made the church itself a trigger for him. Sexual abuse can cause PTSD & being in or near a church is likely to cause flashbacks or anxiety due to the abuse he suffered.
One of the first steps to getting him to attend church would be to appropriately deal with the trigger aspects so that he could be comfortable even sitting in church without reliving the horrible abuse he had to endure. That may entail starting off by going to a church parking lot when there are no services & being allowed to talk out his feelings about what happened. Maybe just sitting in the church while empty. Having a minister re-affirm that what happened was horribly wrong, that he didn't deserve what happened & in fact, it should never have happened especially by someone using the church as a hunting ground may also help when he is physically in a church to not get overwhelmed by the feelings of the abuse itself.
There are lots of good resources even online to help him be able to process appropriately that terrible trauma. When that happens, his heart may be more receptive to seeking God. He doesn't need to go to a church to open his heart to God, which is what you ultimately want. Maybe baby steps like watching the Christian channel on TV will help him deal with his triggers & feelings in a safe environment in a helpful way if he's not ready to subject himself to being in a church building.
Here are some helpful links: Psych Central: Abuse: Support Groups sexual abuse of boys
It is well documented that as many as 1 of 3 girls is sexually abused before she reaches 16; what is still not widely known by the public & much of the psychiatric community is that as many as 1 in 5 boys are sexually abused before he reaches 16. This statistic was quoted from Matthew Parynik Mendel's book "The Male Survivor: The Impact of Sexual Abuse." Sexual Abuse of Children - ChristianAnswers.Net
Because some of my abusers were “upstanding” members in the church clergy, I couldn’t trust a God who seemed indifferent to my suffering & who allowed adults to abuse me. I was afraid of that kind of love, so I rejected God & the counsel of the church. Clergy Sexual Child Abuse-Myths
Isely (1997) wrote his dissertation on the effects of clergy abuse, interviewing 9 men who were abused by clergy as children. Isely described symptoms of posttraumatic stress, anxiety, guilt, low self-worth, loss of religion, anger, difficulty managing & maintaining interpersonal relationships, & depression. These aftereffects are consistent with sexual abuse survivors who were abused by a family member, family friend, neighbor, or other trusted adult. Genesis Consultants: Sexual Abuse Recovery
Male Survivors of Sexual Abuse face the same problems women survivors face with two exceptions--they judge themselves more harshly, & they have a very hard time recognizing they have been abused.
Men's indoctrination since childhood dictates that they are to prove their sexual prowess. .... Additionally, men are indoctrinated to defend themselves against all odds--to fight to the death to protect their manliness. They are expected to risk their life or sustain severe injury to protect their pride & self-respect. These distorted beliefs about manliness & masculinity are deeply ingrained & can lead to intense feelings of guilt, shame & inadequacy for the male survivor.
Both male and female survivors generally question whether they deserved or somehow wanted to be sexually abused; they believe if they failed to defend themselves, they must have wanted it. Although both female & male survivors frequently view their abuse as a loss of manhood or femininity & are disgusted with themselves for not fighting back, men judge themselves more harshly.