There is a number of reasons as to the why?
From the top of my head, media, general public, Congress and Executive are ignorant as to what science can do and what it can't, thus a chunk of money is going to generally poor effect. Another thing is that Innovative solutions are not provided money to seed itself and grow. How could it if both the Executive and Congress don't have a serious strategy for prioritizing problems, as well as finding private sector partners for funding. Last but not least is that too much money is spent on military science and military research.