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Showing compassion may be the hardest part of dealing with your roommate. On the one hand, you may not feel a lot of compassion, so that being motivated to be compassionate can seem impossible. At the same time you may not meet with a warm reception in your attempts at compassion, so that you may feel rebuffed or just a failure if you don't have "success" in your efforts. However, if you focus on your responsibility to show compassion rather than on your feelings or on the other person's reception, you will find it a lot easier (James 3:17-18).
Compassion involves caring about those aspects of your roommate's life where and when you can -- caring about what they care about, sorrowing where you can and rejoicing where you can. Obviously, as with all people, your roommate may rejoice in sin or despair under conviction, and you may not find it appropriate to rejoice or sorrow with them in all instances. Still, there is likely a lot more to your roommate's life than rejoicing in sin, and these are circumstances and instances in which you can care about a fellow human being without requiring ideological agreement. Jesus did not wait for us to agree with him that we are sinners before he showed us compassion. On the contrary, "This is how God demonstrates his love toward us: while we were still sinners, Christ died for us" (Romans 5:8).
Sometimes if your religious convictions are known to others, folks will have (understandable) assumptions about what you think, feel or believe. Often the relative importance or particular place homosexuality holds in your own world view may not be immediately apparent, and the more you talk about it the more likely it will appear to others that it is a colossally big deal in comparison with other issues in your mind. Without trying to prove that YOU are RIGHT, you can try to help your roommate understand why you are uncomfortable, why OTHER issues make you uncomfortable, etc. At the same time, you might want to go out of your way to demonstrate clearly how you don't fit an evangelical or fundamentalist stereotype of hatred, hypocrisy, etc. Where you DO fit such a stereotype, you can model repentance and humility, putting your own sin in a perspective your roommate (by God's grace) can understand.
Include in Your Life:
If you are uncomfortable with your roommate, without realizing it you may be withdrawing yourself from that person in such a way that he or she may feel excluded. While this may not be your intention, what you communicate to someone when you are reacting unconsciously out of personal interest is that such people are to be avoided. They may notice you don't talk with them about the same things you do with others, that you act differently, do different things. You can go a long way towards relieving tension and living out the gospel just by deliberately including your roommate in on all kinds of things in your life. Talking with your roommate about your relationships, your fears, your goals, and your questions can show that God's people can welcome him or her into their lives without being contaminated (Luke 15; 1 Corinthians 5:9-10).