Well it didn't really last all that long, just most of Senior year.
I think it was probably just a side effect of them being thrown together so much as part of Mystery, Inc. Anyway, She got Shaggy cleaned up, and was picking out his clothes, until finally he said enough is enough. So they went back to being "just friends".
For some reason she said it was Scooby's fault. I can't see how the poor dog could have done anything.