I don't mind it so much. They somehow managed to make it sound worse by Season 3 though. The up tempo beat doesn't match the crew going through their dark night of the soul.
I'd have liked to have seen them keep changing the theme tune and opening titles every year. Take a look at the Mirror Universe two-parter and it pretty much confirms how successful, radical change would've been. Do something different each year after the history of exploration montage.
Gradually by the final season, have it end up beginning to blend in with 'future' Star Trek shows. Starfields, ship flybys and Scott Bakula saying the "To Boldly Go..." mission statement.
That's an interesting idea, to have the theme music progress along with the general plot outlines.