A multitude of reasons. But mainly: because they are HARD to do well.
I'd say 99% of the submissions I receive with a prologue don't need it. Most of the time they read (to me) like: look at me! I can write an AMAZING scene - oh, but...sorry, you have to read 100 more pages to get to it.
What a prologue should NOT be:
-from a POV other than the main character
-a false start
-an attention grabber
What a prologue SHOULD be:
-an introduction - which means the story will CONTINUE FROM THAT POINT, not 30 years later
-A preliminary act that sets the ACTION of the novel into play - NOT the action itself displaced into the first three pages
-A method to call attention to an important THEME
In ancient times, a prologue was used to describe events that took place prior to the opening scene. They could be supplementary to the text. And if you're writing the next Canterbury Tales, by all means; ancient prologue away.
But if your style is grounded by more modern methods - nix the prologue, please.