Judging by a couple of posts early in this thread, at least some FTers don't get how corporate loyalty programs work, so I'd be surprised if the OP's colleagues all do. So, I agree with previous posters: education is key, especially the fact that using the corporate program doesn't affect their personal miles.

As for motivation: I think the OP addressed that in post #3. The fact that it's a non-profit, so employees have some interest in what the organization does, and that the use of corporate miles is visibly good to them, ought to be enough. I think non-compliance is more a combination of (a) lack of awareness and (b) the concern over losing individual miles. Again, education is the answer.

(I once ran a consulting firm that had similar issues. Once people understood what was going on, no problem.)