http://news.ycombinator.com/item?id=837462 - the answer to your post - sums up nicely why they are annoying: they make it so that one line of code is often not interchangeable with the next, so when you refactor or cut and paste, you have to go fiddle with line endings.
I've already posted http://news.ycombinator.com/item?id=837217 to express my opinion on that though, if you want to read it.