Generally speaking when someone says: "It's not you it's me" it means they don't see you as being "the one". They may even care about you but they're not "in love" with you and never will be.
More often than not they're letting you know they've decided to move on. By saying "It's not you" they're trying to avoid a situation where you might (beg or promise to make changes) in yourself.
Essentially they're telling you: "There is NOTHING you can say or do that would make me want to stay with you!" "You're not the one!"
As much as people hate hearing (it's not you it's me) the reality is there's more honesty in that statement than many others. It is (them) that has changed or have decided they'd be better off without you.