Yes: The League has often turned a blind eye to PED use.
Bud Selig has been heavily criticized during his tenure as league commissioner for a number of reasons, but his most glaring deficiency has been his inability to come down hard on dopers in the '90s and early 2000s. Selig would literally have had to have been blind to not see how huge guys like Jose Canseco and Ken Caminetti were getting. Bud, you really thought they got those muscles from a new offseason diet or something? Selig was happy to let his players' questionable behavior slide only because they were boosting interest in the game again, and driving TV ratings up.
Since 2007's infamous Mitchell Report was released, though, Selig has pledged to rid the game of any influence from PEDs, but from this latest steroid saga, it's clear that his tactics have either failed, or not been harsh enough. Whether they were incompetent or just didn't care, the commissioner's office has been just as complicit in all of this wrongdoing as the players have. With guys like Selig in charge, this situation will never improve.