Well, when it comes to movies or tv, I know for me, it really depends on the scenario. I often ship due to good potential romantic chemistry between characters/actors. Other times, I just don't want them to pair up, not because they don't have great on screen chemistry, but just because the characters themselves work so well as friends or enemies, I think it would break the story line.
Personally, I don't mind people shipping my characters. I find it interesting the relationships they find between the group of characters. Sometimes, it helps me see angles in the story I didn't know existed. Not that I'll pair them in the end, but it's interesting to see the potential the characters have within the group dynamic.