Because the patent examiners don't search source code. They only have a ridiculously short term to research a patent claim (about 8 to 10 hours over a period that could be two *years*), so they tend to search a limited set of prior art and existing patent applications.
Patent examiners are not lazy: they are just extremely overloaded with work, so they simply can't decipher all code out there, and stick to the things they know are good prior art.
What we (disclaimer: I work for Open Invention Network) try to do is to make a good source of explicitely documented prior art of open source software. We submit the defensive publications we receive to a database on IP.com, to which many patent offices are subscribers.
This is not about doing a patent examiner's job and your suggestion about getting paid for it doesn't make any sense to me at all. It is about protecting your own freedom to operate and help patent applications for which prior art exists to be rejected, or decreased in scope.