They didn't hate each other. They respected - and were even fond of - each other. Until his death, Ebert continually quoted Siskel and referred to the latter's insight about various films.
That said, they were (friendly) rivals. And rivals spar. Here's a pretty good glimpse at their relationship:
Bottom line: spend decades together, and tempers will flare. Ask Metallica. Ask brothers. Ask any married couple. Harsh words and an abrasive tone do not imply hate. If anything, they suggest a longstanding familiarity.