That's not how our brain actually works. The stuff we read/watch influences us greatly. There have been a few psychological studies done on this and the results were scary, we think we can control our attitudes and norms but it is shaped by everything we do. So yeah, those themes are not innocent just because they aren't real.
Yes and no. I wasn't saying that the themes were innocent, just that most people can separate fantasy from reality, and because of it, use it to escape from stresses of real life. I've had some pretty fucked up dreams, and that's my brain de-stressing, but when I'm awake, there's no way I'm going to do what I just did in my dream. And yes, humans can be influenced. Some more easily than others, and in many varying ways. I read yaoi of all kinds - sometimes it includes rape and shotacon, but I'm not so influenced as to want to do it myself. Our brains are too complex to say that just because we read, see, hear, or dream something, we're going to act out on it. As humans, we have the ability to reason and to make choices based on what we are taught is right or wrong. Yes, there are people who don't have those inhibitors that tell them to stop - so unfortunately, they can be dangerous when influenced.
I'm pretty sure I'm not going to get a sex change and butt rape a man after reading this.
So basically manga became the new Las Vegas, literary edition.
There will always be manga with topics that to many people are obscene, vulgar, taboo. Rape, lolicon, shotacon, tentacle porn, beastiality, and also lesser evils such as cheating or panamorous relationships, etc. Part of the reason is that the Japanese culture and society are experts at keeping their real lives separate from fantasy, they are expert at keeping love, family, work, and sex separate (in any of those combinations), and because of the extreme pressures they are subjected to in school and work, they use it as a form of release. They read hentai manga because it's a way to experience the taboo without actually getting involved in it. And because it's a made-up cartoon version, for example shotacon vs actual child pornography, manga rape vs real rape, etc, it's not as risky (and much easier to access). Their regular, boring and monotonous lives are untouched. I was reading an article somewhere (can't find it now) about the Japanese attitude toward some of the themes in manga, and to sum it up I guess, it would be, "What happens in manga, stays in manga."