Commerce is considered evil. We're sensitive to this at JCVI, because a large proportion of the biology research community hates our founder, Craig Venter, for having had the gall to make money off of biology. Today, it's better-accepted; but when he started, it was apostasy.

If he hadn't made money, there wouldn't be a JCVI now; we couldn't afford to do what we do just on grants. By its fruits you shall know the tree.

Universities are given a free pass in some ways. Note that the first universities (Padua, Paris) were deliberately for profit. Harvard would make a profit without charging any tuition - so why does it charge so much tuition? MIT may be in the same situation; they get over a billion dollars a year from the government, and have only 10,000 students.

Many of our grants require us to give the results away for free. If we charged people to run the software on our servers, we'd have to make the case that charging for the use of computer time was distinct from charging for the use of the software resulting from the contract. There's little legal precedent in this area AFAIK. Moreover, legal precedent don't matter when you don't get a chance to make your case - it doesn't matter what the law says; it matters how the next program officer feels about what you're doing.