He knows that it's time to call it quits because he had let her down too many times. They tried to make it work, but mole hills turned into mountains before they knew it. Things just piled on and led them towards the end of their relationship. Thus the lyrics:

"When did the rain become a storm?
When did the clouds begin to form?"

He still finds her beautiful even when she cries and mascara's running down her face. He still cares for her even when they've broken up.

God, I love this song so much.