The Sorting Hat puts you in the house that has the traits you value the most, not what you have or represent.

Example: Hermione does value intelligence and learning and curiosity like a Ravenclaw, but she specifically states at the end of Sorcerer's Stone that she values courage more. Neville is another example, he wanted to be in Hufflepuff. He asked the Sorting Hat specifically to be placed in Hufflepuff, but was placed in Gryffindor because he valued bravery and courage more than loyalty (which to be fair could work for both houses) and kindness, which is proabably due to his parents. Peter Pettigrew is also a prime example. He did not exude any of the traits of Gryffindor. But he valued them more than anything else, which is evident by his absolute worship of the other Mauraders. He valued what they stood for in his mind, which is something he desperately wanted to be but simply wasn't. Dumbledore is along those same lines, with having qualities from another house but not valuing them as much as others.