I think that Cavendish would have held the green jersey had the route been similar to last years. Last years route had six flat stages before the first mountain stage. These stages would have suited Cavendish's stregnths very well.
This years tour had a lot of uphill finishes early on or Cat3 or 4 climbs right before a short downhill finish. Oscar Freire, who is a former world champion, is more suited to these stages than Cavendish, and was able to score many points on these stages, whereas Cav didn't score any. Early on, the green jersey was held by riders better suited for climbing such as Valverde and Kirchen than the sprinters .
Boonen wore the green jersey early on last year. I don't think he would have done the same this year.