It depends on what you are seliing and that might be part of the problem.
I'm not fond of PayPal either mainly because as well as the fees for the listing off Ebay you also have PayPal taking their cut, so less for me. But recently I wanted to sell some computer games and they would not accept the listing unless I accepted PayPal as an option, because of the amount of copied games on the go they said. I think its more because Ebay own PayPal and want to increase profits but thats my opinion only.
Anyway I wanted to sell them so had to accept PayPal as a method of payment.
Regarding the not accepting cheques I don't know as I have never done this, I assumed you could just untick it.