It's got to do with the evidence. Why would these two characters risk so much for that kind of connection when, you know, they don't have to?
Now, I can give a lot of reasons as to why I think these characters were made for each other. A lot of reasons! Two sides of the same coin. Checks and balances. They're hot. But I find it really, really hard to get to a point where they have a basic understanding of their motivations and reasons beyond a physical attraction (and the physical attraction thing gives me pause, too.) I am often falling back on the "I don't know" version of the answer to 'why?' (I do think that this can be true to life. I don't always know why I like someone. But. It helps.) And this doesn't satisfy me. It doesn't provide me with enough to sustain an ongoing narrative; not one that's mostly about their pure, pure love, at any rate.
Gene, strangely, I have less trouble with, because I think Gene knows himself very well --- a hell of a lot better than anyone else does. But Sam is my default point of view character. And Sam is also a moron. He's self-involved, but with little to no self-awareness. I end up with these fics where Gene's all assured; either in his misgivings of the relationship, or his willingness to take that leap of faith, but Sam's largely in the dark, and as a consequence, so is most of the audience.
So. When I write Sam/Gene, I either decide to ignore reality for a while; forget about the evidence, not bother with the struggle, and go straight for the loving (and hate myself in the process.) Or I try to show why they love each other in all types of ways (and this requires plot! oh so much plot that makes my brain hurt, so I get weirdly angsty because I'm still on A and B is really far away.) Or I become a miserable git (and wonder why this sworn romantic is such a miserable git.)
Huh. After three years I finally get it.