This was already covered in another thread. One of the Ford customer service reps that was on here clarified that you get free upgrades for every new release (2.4 -> 2.7 -> 2.8, each upgrade is free) but if you have to reflash one, so 2.8->2.8, it MAY not be covered. That kind of depends on the dealer and how much noise you have to make.
This policy may change for the better or worse, but we don't know yet.
I don't have my Explorer yet, hoping this week, but still looking forward to MFT. I still think having it is far better than not having it, and the time I have spent with it has been pretty great. My iPhone 3G had bugs and that for the first year, apps crash all the time, etc, but they got it worked out and running pretty damn reliably between year 1 and 2. They may have rushed MFT, but I have confidence that Ford and their partners will get this worked out in time.