'Nice guy' is one of those thigns where the meaning varies. My year 1 teacher hated the word nice and refused to let us use it in our stories, she told us that it had no concrete definition and that we should be able to substitute it for a better word. (Not those words, but you get what I mean).
I call lots of guys nice. Nice can mean they were sweet; read as did you a favour. It can mean you are not their type and they are hinting; read as I like you, but as a friend. etc
But in this instance you were dating and thus I would narrow down the meanings to 2.
She could either mean that she thinks you are nice, and because of an insecurity (and don't say she isn't insecure, even if she doesn't appear so, girl's are good at hiding emotions/feelings.) she believes she doesn't believe you, because you are so 'nice' (read nice as good, kind hearted, sweet, etc).
If this doesnt sound right, then maybe it was because she thinks you are too nice and don't act enough like a boyfriend, or that she has realised she likes you as a friend - not more then a friend. If this is the case then as much as it hurts you, its hurting her.
Anyways hope thats understandable.