Jquery + Rails problematic, is that true?

I saw comments in a previous question saying that it is best to use Prototype with Rails. However, my own experience is that Jquery is a superior Javascript library. Being new to Rails, I have not yet investigated how to use Jquery with Rails but I assumed this would work. Is it correct that this may be a problematic combination - especially in relation to Ajax - and that I may need to use Prototype instead?