The difference with racism in anime/manga is that it is almost 9 time out of 10 stems from a position of ignorance rather than any intention to depict a group of people in a specific way. Not saying that at all justifies it, but I think it's different than how we generally see racism in the west. Now I was only in Japan for two weeks, but I can say during that time I think I saw 2 black people. Meanwhile, I saw handfuls of Muslim people (at least going by the way people look/dressed). I think that there is just a very, very low amount of black people there so they only have rare personal experiences with them.
Also, I do think there is progress being made, albeit at a slow pace. For example, Bacanno! and Durarara are generally seen as having more positive depictions of black characters. There is also an anime that came out I think last season, Run with the Wind or the like, where a black character outright calls out discrimination when another character assumes he is a fast runner.
But then you have instances like in the recent manga by the author of Kuroko's Basketball, Robo x Laserbeam, where he added in a black character who was pretty well done, but then he drew a color title page that showed the character as a ferocious ape (because he was going against the main character as a tough opponent). The image on its own is not a bad image, but for a western audience it was not okay at all. Any westerner could see at a glance that it is definitely racist. In fact, Viz, sadly, ended up cutting the title page completely from the comic. I only read it in the magazine, but I assume the print had it cut too since they censor absolutely everything and anything.
I'm putting the image under the cut here:
It is definitely an issue and I do think it's important that, before people bring out the pitchforks and torches, the instances are addressed so they become more understood. The more people understand, the less likely it is to happen.
I think it will still be a number of years though until we stop seeing this kind of imagery/poorly depicted characters.