All the bad stuff you can find about him is false or presented in a misleading way, by either pro-Putin propaganda or people who likes to get triggered by clickbait titles.

E.g. about the Muslim related thing: because the ad in question featured a photo of Chechen (?) soldiers, and the message about the right to bear arms was worded roughly as "you should be able to defend yourself from cockroaches", clever people decided he compared Muslims to cockroaches. Even to this day in Russia, Chechen people are massively (and rightfully so) considered dangerous, and bearing arms is not legalized. I watched him for years and Muslims were never on his agenda. The ad was created in 2007 and available on Youtube on his personal channel to this day. Guess not enough Muslims were upset about such "calls for genocide", heh. There is another ad about illegal immigrants and they too are still a problem for Russians.

Personally, I think he was the best politician of this time, maybe not only in Russia. Having watched him for years, there was never an ounce of radicalism or otherwise calls for unfair treatment of anyone. There were points to disagree but he was always open to public discussion and debates. They are correct when they say he was a hero Russians need but didn't deserve.

tl;dr: Navalny was against criminals, not Muslims.