The new good books
I'll admit I've never read a Harry Potter or Left Behind book, but Slate does a solid job in pointing out the similarities between the two series, and noting the big difference between the two (which probably helps explain some of the attitudes toward the books):

Left Behind is Christian and Harry Potter pagan, but rather that Left Behind is Protestant and Harry Potter is Catholic. One of the chief theological arguments between Catholics and Protestants has been over whether salvation is earned through faith or by good works. ...

Left Behind is fatalistic; Harry Potter sees outcome determined by individual actions. Both provide a roadmap for how to live a good life, but in one case the key is morality, and in the other it is faith.