Having just spent the past two days reverse engineering an API that used protocol buffers, I can tell you I would have much rather done it against XML. :)
As for parsing, I guess I don't get what the big deal is. I've long since given up on SAX parsers and occasionally use pull parsers, but for the majority of applications using a DOM parser gives you a very OO friendly approach to turning that XML into your objects, and it is dead simple. Sine the generated Protocol Buffer objects are immutable and can't be used as base classes, I suspect the amount of code to turn a 'message' to your domain objects and vice versa is very similar between protocol buffers and a DOM impl. At least it has been in my experience, neither is hard.