The recent graduate said that when he brought the charges to the academy's Military Equal Opportunity Officer, the officer told him he was a Christian and that it was his duty to "bring him back" to the flock.
"That basically hit my complaint on the head," the recent graduate said.
Though some say he was slow to act, the head of the Air Force Academy, Lt. Gen. John Rosa, is now taking action. "Quite frankly, some of the incidents that we looked at and heard about over the last four or five years were vicious," Rosa said "And that's totally unacceptable. It's not part of our profession of arms."
Rosa told the academy's oversight committee in Washington last week that he's instituting mandatory classes on religious respect for cadets, faculty and staff. "Just like sexual assault, we do not tolerate this kind of behavior," he said.
But David French, who runs the Foundation for Individual Rights in Education, a nonpartisan watchdog group that monitors free speech on college campuses, said there's no comparison between sexual assault and speech, no matter how offensive. He said the academy must not trample on the rights of Christian students in trying to fix this problem.
"A cadet can constitutionally approach another cadet and even say, 'I believe that my beliefs are the truth and the only way to go to heaven, and yours are sending you to hell,'" he said, "and that's constitutionally protected."
Curtis Weinstein, for one, said he's satisfied with the administration's response so far, but he will not forget what happened.
"The reason why it's been going on for as long as it has is because most of the upper leadership and some of the teachers and a lot of the cadets, of course, are Christian themselves," he said, "and they didn't see a problem with the culture how it was until, finally, we're getting together now and, yes, there is a problem and we want some things done differently."
Rosa recognized the need to tread the fine line between protecting minorities from abuse and censoring the Christians. He said recently: "That's the last thing we're trying to do. That's what we're defending. That's why we wear this uniform, so you can believe."
ABC News' Dan Harris filed this report for "Good Morning America."