If I had to guess, it's because he doesn't want to sue a company he has a stake in. That's like suing yourself. Patent and intellectual property copyright is a funny thing; the owner can enforce (or try to get it enforced) when they feel like it. They usually let it go when it's to their benefit.
It's obvious why - nobody said patents were "fair". The patent holder has his own discretion.
He's not suing microsoft because he'd be shooting himself in the foot. He might have a deal with them to license it, or he may just be letting it slide (he can always sue them later). Same with google.
He's under no obligation to enforce his patents - it's up to him.
FTA: "Notably missing from the defendants' list are Microsoft, in which Mr. Allen remains a major investor"