Some of the philosophical movements definitely qualify. Cynics and stoics as well as various other philosophers were banned from Rome at one time or another. Of course, stakes were a little higher for Romans than for American hippies and anti-political feelings could end up getting you killed.

The elegists have also been read as a counterculture, since they reject politics and martial values. Exactly how true their resistance is and whether or not it was a literary persona or an actual subversion is up for debate. Still, it was taken seriously enough that Ovid got banished.