There's a difference between "we'll guard you against arson", and "Nice place you have here. But it looks flammable. My pal Vinnie here has a bad habit of starting fires in a place like this. If we can come to some arrangement, I can make sure Vinnie doesn't come around here."
The basic idea, as far as I can see, is that if there's an IP problem with Ubuntu, either Canonical is going to get sued anyway, or some IP troll is starting its campaign by shaking down customers before tacking someone who'll actually fight.
"We'll defend you against our common enemy" is pretty significantly different from "We'll protect you from our litigious buddy Microsoft". Especially when the latter promise is not effective against other claimants.