Actually learning about another religion/culture can do nothing but make you a more educated, more well rounded person. It may even reaffirm ones own faith because of the differences.
If someone seriously has their faith shaken by a cartoon, then they didn't have much faith to begin with.
Or try watching Dogma, that will rattle your thought of faith for sure.
Spiritual health is not a monopoly of Abrahamic religions.. It NEVER was. They just think they do.
The truth is, some Japanese animation feature some of the country's culture and everyday living. Amidst some of the violent and unwholesome themes, we get to familiarize ourselves with what people in Japan believe in and how they go about with their lives. It can be informative. Maybe not always "spiritually enlightening", but hey, at least we learn something. Besides, most Japanese Aime can be quite philosophical and intelligent.
Any person who is a hard line supporter of the belief system he/she aligns with will find some Japanese Aime quite repulsive. It will not be just the Christians, Jews, and Muslims.., but even the "less popular" religions not aligned with Shintoism. And yes, even the hard line atheists will not see them as a good thing.., they don't even believe in spirits.