Haven't read the full interview, but from the quotes I've seen, it sounds like he's just having a go at Pep, not City. Of course, Pep as manager is an important part of the club at this time, but I think a few are extending the attack to make it about the club.
Personally, I'd be surprised if it were true, Pep's has frozen out and sidelined African and non-African players alike. For every Yaya there's a Hart, for every Eto'o there's a Deco.
I'd suggest that Yaya is bitter about initially being frozen out last season and then with the limited role he had thereafter. He's looking for justification and his ego won't allow him to admit that it was because his attitude, fitness and athleticism were lacking. So he's looking for a non-footballing reason and has come up with the idea that Pep doesn't like him because he's African.
I don't like it, but I'm not going to judge him for it. I'm a white male from a working/middle class background and have very little idea what it's like to be part of a social, cultural or ethnic group which has historically suffered from persecution or discrimination. If someone does belong to one of those groups, it must be very tempting for them to assume that that's the reason they're failing, rather than admit to themselves it's because they're just not good enough or working hard enough, etc. Especially when they've been as good as Yaya was.
On a side note, whatever he says off the field, he'll still be a legend in my eyes for the things he did on the field.