I think it's a great thing. People already use Azure or some other provider at these institutes (I know my uni does). If Microsoft wants to trade free services for market share, everyone partaking benefits from it -- unlike cigarrets at schools. If you or your institution don't want to partake, don't. I know I won't.
But there is no reason the support has to be "free" access to cloud resources at all. Why not just donate the money and let the nonprofits choose which cloud to use (or whether to use a cloud at all)?
Would you mind explaining how one can create value merely by donating?
First, you're not giving away physical goods, but eligibility for a service - but what exactly this service entails and how useful it is can still change in the future.
Second, it's a service that requires a substantial level of commitment from your clients - a commitment that causes risks for the clients in its own (lock-in) as discussed in many other places in this thread.