I don't know if this is true, but it seems that these Communists are comfortable with the protests being Communist. I would be afraid of either group appropriating the protests if I were in São Paulo. I didn't get the impression that this was a Communist protest. Is it possible that a protest against corruption and for fair use of tax dollars could be considered without assumed sympathy for established and storied left-leaning parties? If so, establishments on both sides of the spectrum poison the waters. This is tangential to the matter at hand. I imagine it's very possible that parties on the right are trying to co-opt the protests in Brazil. However, both the Communists and the Fascists have a long history of implementation through oppression. I'm quite liberal, but to me personally, associating with Stalin's party is as distasteful as associating with Hitler's party. Personally, I'd love to see a new progressiveness that has no tolerance for legacy code.
I think you have a misperception of modern communists. I've never met a communist that endorses Stalin's policies. He's recognized as historically important, which is pretty much undeniable, but many communists today consider him (and sometimes Lenin) to be state capitalist. Modern Western communists are very much towards the libertarian side of that particular political axis. Ironically, communists today kind of have a problem where accusations of Stalinism have become a thought-terminating cliche. edit: this is not to say that i agree with modern communists. there are significant problems with vanguardism, democratic centralism, and other ideas which are still endorsed by the communist parties of today.
the branding problem is being solved as we speak. newer generations are less indoctrinated by the cold war propaganda that created the branding problem. anarchists are developing new theory all the time, orthodoxy is antithetical to anarchism. the student group that organized the initial bus fare protests is considered autonomist, which is a newish strain of anarcho-communist thought that developed in the sixties.
Speaking of anarcho-communism, these protests have led me to do research on the anarcho-syndicalist strain of anarquism.