Actually, by discussing this perceived biased against the Christian curriculum, you're showing liberal institutions that you are exactly what they DO want. You'll bring an atypical background to their campus, but you're also savvy enough to be aware of what goes on beyond your living room. A less-informed home-schooled student might not even realize that such prejudices exist.
So, here's what I suggest: At some point in your application (in your essay if appropriate, supplemental letter, "additional information" section, etc.) explain the curriculum you have pursued, but also point out (ideally in a humorous and not defensive way) that you know that your academic background may make you an anomaly on campus. Acknowledge that you're aware that some classmates might toss tomatoes your way when they hear "Bob Jones." Explain that you've been able to discern both the pros and the cons of these teachings, and that one of the reasons you've selected [name of purportedly prestigious school] is because you are eager to interact with students who may have come of age in an academic and religious climate different than your own.
Above all, don't worry. Colleges really do seek diversity, especially when it means accepting students who have an awareness of the world that extends past their own little corner of it.
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