It may be that they are actually using the wrong word. If it is being used in connection with "I'm not interested in dating you" then chances are what they mean by "too nice" is "too much of a push-over." And for the record, most people don't like hurting someone's feelings, I know, because I was in that situation many times.. how to let a guy down as nicely as possible. When you don't know the guy very well, you you don't want to be brutally honest because the guy could be a stalker, psycho, etc. I had one guy call me and harrass me after I was more "honest" with him as to why I didn't want to see him. So I can't blame women for playing it safe.
If these are good female friends of yours not being honest, that's a bit different.
My response your your question may not be liked by many people, but I'm trying to be as honest as I can with you as a woman. You should never change who you are or your values for anyone, but as to why being too nice is a turn off with some women its because women tend to like men who are confident and decisive.... it would appear being too nice runs contrary to those attributes.