Comparing baseball to other sports is apples and oranges.
Firstly, MLB is subject to special regulation by congress because of its special anti-trust exemptions. If baseball doesn't comply with congress's wishes, congress can yank the exemption and there'd be the possibility of competing major leagues.
If you want to attack the NCAA on the basis that it's a monopoly and needs to be busted up, fine. That's another issue that the Utah attorney general is looking into. But that argument fails too, for one important reason: the NCAA is powerless without the assent of its member institutions. The schools created the NCAA and can choose en masse to get rid of it if they so desire. "BCS conference" institutions are far outweighed in NCAA membership by their poor little unfairly treated brethren.
Secondly, congress investigated steroids in baseball, not fairness in baseball. At their essence, the baseball hearings were a public health issue, and there's a rational basis for the regulation in that area.