I personally have had pretty much 0 problems after the implementation of PunkBuster. I have a IP Blocking program (PeerGuardian), Anti-Virus and Trillian running while I play, and I have yet to encounter a single problem, other then the maps taking a tad longer to load but I figure that's the fault of my crappy PC having to work a little harder.
These "people" are having problems because of these things:
1. They insisted on modifying game files (skins, etc) and kept them on after the PB was put on. Now they are boggled as to why it won't function correctly.
2. They don't have their internets/routers/firewalls configured properly, and it's causing some problems with PB.
3. They just put it in, there's bound to be problems.