No matter how detrimental software patents are to the big players, they are far more detrimental to the small players. If it can keep the smaller players from being real competitors, it's in the best interest of the big companies to just pay the patent tax. They stand to lose far more with a lower barrier to entry to their markets.

Software is kind of unique (and even moreso now with the prevalence of cloud providers) with its otherwise low barrier to entry; as capital expenses are extremely low compared to other industries.