I've seen a combination of factors. Relative power has an impact on reputation and alliances, an ally will dislike you if you rise faster than him. Contact has an impact, as I find over time relationships degrade all by themselves if you don't shell out the occasional 500 "Remember me ?" bucks or have any kind of diplomatic contact. How you play definitely has an impact too :

I once as the HRE was in good standing with all my neighbours and the Pope (not a small feat in and of itself I might add). Then I decided on a lark to invade Denmark, with which I was not allied mind you, we only had trade agreements. While the Pope backed me at first (I had full meter and a history of church building, the Danes did not.), over-time my pope-o-meter started to dwindle, which angered me a bit since my good, upstanding christian image and faith was being sullied, an image I had spent quite some cash on too. All the while I was still Friendly to So-so with the rest of my allies.

I then in the same turn moved on the Danish capital, defeated on the way a large Danish army taking *lots* of prisonners (including an heir, IIRC), executed them all and sieged Arhus. Next turn, I assaulted it, killed the king and burnt the city to the ground (slaughter population. I was in that kind of mood). Every other Christian faction instantly hated my guts, and so did the Pope. I was still listed as trustworthy, only I had become that generation's Rogue Empire of Evil, I guess. But in a trustworthy way. The Muslims didn't seem to care that much.