Yes, few mutations are beneficial, and it's the role of Natural Selection to weed out all the bad ones. We must also not forget that the vast majority of mutations that occur naturally are completely neutral and simply just accumulate as junk DNA which takes up roughly 95% of the human genome.
Although, my favorite part of the TMNT is how they're some of the few superheroes that seemed to have some negative consequences from the mutation - you know, the whole hideous-abomination-of-nature-living-in-the-sewers deal. They didn't get heat ray vision or anything. Awesome.
Now Spiderman, on the other hand... he could use some cancer from that spidebite.