the reason is that the riders are just the hired help. The team management represent the real money interests. Clearly there have been teams with systematic doping.
And you are right that only by penalizing the teams will the sport ever clean itself up
Having the sponsors leaving in droves over the last couple years is certain to help the process. I think the fact that the 3 big new sponsorships went to teams with in-house drug testing and anti-doping controls will be the example for moving forward