Secondly, while I was writing some fic feedback-feedback, I started thinking again about the whole "ship as a function of plot vs ship as a function of character" thing. Yam, was that you I was discussing this with? Anyhoo, I think it's part of the reason why there are people out there who are open to reading Sam/Jack but can't find a fic that is 'believable'.
I think it comes down to the fact that most SJ writers, being shippers themselves, see ship as being a function of character. That's why the smallest scene between Sam and Jack can be termed shippy (whether or not she says yes ;)). Under this, let's say, "model", ship is inherent because it is an accepted part of the characters. Shippers go into an episode or a fic with it already firmly in mind that Sam and Jack have feelings for each other which they would act on if only the right trigger could be found. A great deal of shipfic - at least the subgenre that concludes in a Happily Ever After - is the search for a palatable trigger.
Meanwhile, you have the non-shippers. Not anti-shippers, not people who feel sick at the very thought of Sam/Jack who would rather gouge their eyes out with hot pokers than read it (sort of the reaction I have to AQ's fic), just people who "don't see it on the show" but haven't necessarily ruled it out in fic. It seems that they would see ship as being a function of plot: a scene between Sam and Jack isn't shippy unless there's actual relationship-related content, and the existence of the relationship (or the feelings) must be explicitly and plausibly stated in fic. Even justified, even though that's a touchy word. A trigger is still required, but it requires deeper roots to be realistic.