Perfectly valid. I, however, think that both grappled with emotion, with being part machine (or technology), with standing apart from humanity, with having social stigma attached to them. They were both more on the analytical side and shared many interests. I think they had plenty of chemistry. I also suspect they didn't get paired because he wasn't conventionally pretty enough. That's just how I feel. Seven and Chakotay, to me, didn't have any chemistry at all. It was so...tepid. Shoehorned. Meh.
But more power to you if you like them together. It's always better to like things, and I try to do that. Mostly, I succeed. Sometimes, though, it doesn't work. This is one of the few instances for me personally.