There are two issues that I can think of, besides the obvious ethical implications.
1) Logistics. Here in Massachusetts, it is required that inmates convicted of felonies have their DNA put on file. This is a daunting task for the State Police, and it is just those whoa re incarcerated for felonies. There is simply not enough manpower or money to do this for all 6.5 Million citizens of the Commonwealth, let alone the 304 Million citizens of the United States
3) Investigative. Contrary to popular belief, there is such as thing as too much evidance. In Forensic Science, ther is something called Locard's exchange principle. It states, in essence, that whenever two object come into contact, something of one is left on the other, and vice versa. THis is tyher basic prioncipal that modern forensic science is built off of.
Now, consider the number of people that you have had contact with in the past 24 hours. Cashiers, delivery drivers, friends, family, etc. The sheer amount of DNA that would need to be tested for a murder victim is staggering.
Related to this is the fact that most Murders are already solvable using conventional detective work, and DNA is usually only used as the proverbial 'nail in the coffin' for a court case.