Software patents often harm the really big companies too, due to the existence of patent trolling companies which exist for no other reason than to horde patents and sue big companies.
That's why Microsoft, for example, pays off billions in patent lawsuit winnings and then hires expansive lobbyists to keep them coming. It's peanuts to big companies but the freedom from upstart competition they get is priceless.
The patent system itself is broken..... let's fix that...