OK, so Boonen is top dog at the moment. He's tough, he can beat 'em on the cobbled nasties and hang in there on longer climbs - and he's a sprinter par excellence. If you can't get away from him it's game over, he wins.
But Le Tour is less about cobbles and more about the Alps. Sure Boonen can hang in there and probably pick up the green jersey but he won't figure in the GC. And look at this - Valverde beats Freire in a sprint (and Freire is no slouch). Lots of true GC contenders in that race too, including Iban Mayo and Cadel Evans. (That's a great report by cyclingnews.com, btw, with excellent shots of humbled riders on the cobbled climbs.)