Meanwhile, I'm completely on board with this. Trello is used by a lot of people who make lots of money and want to throw some of it at Fog Creek because they're awesome, but it's also used by a lot of people who make not lots of money (in some cases zero money) and are organizing things like school projects and community service. (For example, I use Trello to organize all my homework, and a club I'm part of at school…
While your thinking here makes sense, it is better to honor truly Free as in freedom / Libre / Open Source software instead of funding proprietary software. FLOSS is also made by hard-working people and given away mostly and used by people who make money. But if you support FLOSS, your support goes to help everyone in the world, whereas if you fund proprietary software, you help advance something still under exclusiv…
That said, being the heavy FLOSS zealot that I am, I don't have a problem with what trello is doing, per say. They're offering a service, and paying for a service is fine. Particularly a well executed service with good support.
The service they offer isn't just access to an application, though it's a shame they keep that application to themselves, they offer a hosted server and storage for everyone to access. There's nothing morally wrong with it.