The major difference is that Microsoft is probably technically right.
With copyrights you actually have to copy something to violate it. With a patent monopoly you can violate them whether or not you copy anything. Very soon you can start violating patents even if you created the idea first.\\
So whether or not Linux violates Microsoft's patent monopolies has more to do with how receptive the USA Government patent office is towards Microsoft's money then actual merit and it certainly has nothing to with copying or who invented what.