I think it's more that in Season 1, there isn't a lot of intimacy between any of them, but as chemistry goes, it's hard to deny that Sam and Daniel had an instant geek recognition and subsequent cuteness first season. A lot of the rest of the characters really deepened their relationships over the next few years, but Sam and Daniel instantly connected.

AG's point was 'where is the Jack/Daniel chemistry? Where is the Sam/Jack chemistry? I don't really see it' and I more or less agree with her. It's going to take a little while to develop.