Near the end, the steam whistle, which symbolises the boy’s love for the girl (how I see it), is used like this 「それはみんなその小さな汽笛のせいなんだね。」. My understanding of せい is that it has a negative connotation.
So my question is, does せい sometimes, like this case seems to, have a neutral or possitive connotation?
That’s correct, せい is usually used in negative contexts, and though it doesn’t happen often, it’s sometimes used in positive ones as well, which is the case here
Also, as a bit more of an interpretive explanation, based on the context it seems like the boy would like to say おかげで but uses せい instead, thus seemingly portraying the feelings of a boy who is too embarrassed to say it c: