Read this interesting article at rationalchristianity.net to learn several easy ways to keep nonbelievers from visiting your Christian web site. The author took an informal survey of nonbelievers asking them to rate the annoyance level of some of the following on Christian run web sites.
Christian-themed backgrounds (crosses, fish, etc.) Commercialism - prominent ads for online store, "buy my book," "make a donation" "Vote for this site" buttons Using "webservant" in place of webmaster Infighting - "Why Catholics/Protestants/etc. are wrong" Prominent Bible verses (e.g. a theme verse at the top of the home page) Written prayer ("Lord, please use this site..." or "I pray that this site will help you...")
A few comments at the end of the article are also enlightening.

UPDATE: The article points out that these are things you should AVOID if you intend to appeal to a broader audience.