There is a strong divide between people who believe that "non-practicing entities," or owners of patents who are not currently using or selling those patented technologies, are so-called "patent trolls" and those who believe they serve an invaluable service challenging Goliath-style companies' questionable patents.
Part of the problem is the very long time it takes to patent software technology relative to the speed of evolution of that technology. It is not uncommon that an idea -- soundly patentable because it is useful, novel, and contributes to the art -- spreads like a virus between developers and becomes incorporated in major markets well before a patent issues.
Another part of the problem is the appearance by some NPEs of seemingly only being in it for the money. If you are not practicing the patent, how can you possibly have damages that could be remedied by a lawsuit? The NPEs hire Top Gun trial attorneys and engage in aggressive litigation instead of trying to license the patent or find a compromise with companies whose entire business may be built around the technology.
It's tough to generalize NPEs as entirely bad because we do need a venue to challenge those Goliath-style companies. I don't personally believe that a corporation should be immune to litigation or accusations of wrongdoing simply because it is large or popular. By completely foreclosing NPEs from asserting infringement, the system would then be closed to the small inventor who simply hasn't found a manufacturer or distributor yet. He, too, is a "non-practicing entity" on the surface, and he's also probably trying to defend an income stream through litigation. But is he a bad guy?
There are many facets to a specific lawsuit or negotiation -- that's why we have the adversarial court system in the US, rather than just telling people "Well, that's the rule, tough." You have a chance to prove your case, whether you are the non-practicing entity or the company who has been served with an infringement suit.