@zyocuh
Everyone knows religion has caused a lot of harm, you telling him that religion is usually harmful or corrupt doesn't answer his question. Pretty much anyone who knows what manga is, knows religion has been more harmful than helpful. Religion has been portrayed in a poor light in manga for years, and recent news doesn't change that. It's a borderline rhetorical question. The vast majority of the time I see people asking why manga portray religion, nobles, or *insert typically corrupt group here* as unilaterally evil, it's because they're annoyed at seeing the same thing over and over again.
An actual answer to his question would be expand on their cultural values, and systems. Japan doesn't have religion nearly as integrated into their society as the west does, religion has faced and been a source of hardship historically within Japan; there have been bannings of Christianity due to various reasons throughout history, religion, specifically judeo-christian religions, are a severe minority, it's a very secular society, it's a very atheistic society, and doesn't doesn't hold western religion to such a high regard and has no problem turning it into a bogey-man.
Japan, just like most countries, has no problem making obvious external evils into villains, but has a real difficult time looking at their own faults and making villains out of them. Just as Japan does it with religion, among other things. American movies often have foreigners, such as Russians, playing the villain, due to historical conflict with Russia and the obvious corruption within the country. It's a simple, but multi-layered, cultural, and historical issue that factors in many different things. Saying "religion bad" as an answer to his question is not only incredibly lazy, but simply incorrect and not what he's looking for.