First, I'll say that I love brunettes (all hair colors, really). However, Rapunzel looked better as a blonde. Maybe if her brunette hair wasn't quite so short, I wouldn't dislike it as much, and I'm not saying she isn't still cute, but I do think the long, blonde hair suited her better. I also felt like I was seeing a different character in the end of the film and it was hard to suddenly view this person as Rapunzel. I mean, it wasn't a subtle change, like just the color or the cut, it was both, ha. It was sorta like the way people felt a bit detached when Beast turned into a human again, though this bothered me more, I guess because I really adore Rapunzel.
The sad thing is, this could have been avoided. I know they had to cut her hair, but it didn't have to be cut short, and it didn't have to change color. They didn't have to make her look like a completely different person, and it wouldn't have caused confusion with the merchandise (Rapunzel wedding dolls with long, blonde hair annoy me too) and the meet 'n' greet characters in the parks, who are also still the blonde version. They easily could have kept her hair blonde and only cut it at her ankles to keep Rapunzel looking like Rapunzel for the future of the franchise/merchandise/whatever, ha. I know you can argue that they did this for dramatic affect, and that is the most important thing, but I, personally, feel the fact that it makes her practically unrecognizable in the end counters that.
I'm sure Keane and others went over this dilemma while working out story problems.
It seemed like she would've been more distraught over losing what she came to use as a special appendage. Even though her hair was the only real use Gothel had of her, Rapunzel never expressed any interest in cutting it.