Keep the substantive issues the rules (both NCAA's and individual schools') are addressing in mind as well. If you are going with a homeschooling or online program for part or all of your child's education, be sure that it is rigorous, that it covers basic curricula comprehensively, that it has clear standards for achievement, and that it will prepare your child properly to develop and use the higher critical thinking, analytical, and writing skills she/he will need in college. This is more, not less, important for a college athlete -- even with support services, it's tough for these kids to balance everything and do well academically, and it will be much tougher if they don't come in with very firm secondary backgrounds.
I don't know a lot about the various programs marketed for online learning and homeschooling, but in general, synchronous is much better than asynchronous, and opportunities for individualized teaching are very important. And don't count on success on things like AP tests to guarantee that your child is well prepared to ace more advanced college subjects.