(Opportunity) cost. Right now bitcoin mining is starting to require custom ASICs/FPGAs to be worthwhile (although the increasing price offsets that, obviously), because mining bitcoins becomes harder the more bitcoins there are found, so the costs of hardware and electricity start to get very large.

If you had a supercomputer with tens of thousands of CPUs it's probably being put to more scientific use than trying to corner the bitcoin market, which is basically still a gamble at this stage.