I think that most students will treat others with a lot of respect even if they don't agree on everything. Yes, I attend a Christian university, but everyone is welcoming and encouraging to each other. Students are told about Christ's love for them, but they are not pushed. Also, the faculty treats everyone fairly. If a student is uncomfortable going to a Christian school maybe they shouldn't attend, but if they want to stretch their understanding and be thrust into an inviting, loving community they should attend.
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