This always seems to come up whenever Christopher Eccleston is mentioned, so I think I need to draft some sort of standard reply to this question. To that end...
Eccleston left the show in 2005 after serious creative disagreements with Russell T. Davies and the rest of the production team; it's also been suggested that Eccleston's approach didn't mesh well with the rest of the cast, especially John Barrowman's, although I don't think this has ever been confirmed. When he did decide to leave, the BBC floated an inaccurate story that he left because of fears of being typecast; even back then, they apologized and said this was wrong, though Eccleston didn't publicly comment on why he left until 2011.
By all accounts, Eccleston was honored to play the role, not so much because of any particular love for the franchise but because it gave him a chance to connect with and act for children, which is something he hadn't really done before. But Doctor Who remains a really unpleasant experience for him professionally, and he doesn't want to revisit it. I really don't think turning down the role after a couple preliminary conversations with Steven Moffat is jerkish behavior — I'd have loved to see him come back, and perhaps one day he will, but for now it's just progress that he even considered it. Eccleston delivered the one series that he signed on to do, and he did a generally fantastic job of it. While hoping for more from him is all good and proper, he has every right to never appear again, and I don't think he owes fans anything else.