My question got upvoted on Meta but I got no reputation for that. All of my questions which got upvoted on Phy.SE gave me reputation. Any plausible reason for that not happening in this case?
Meta is for discussion and support for the main site, and questions and answers here are not based on physical expertise.
Thus, you don't get any reputation here (but you also don't lose reputation for getting downvoted).
This is the case for all per-site-metas, cf. this meta.SE post. Meta.SE is the only meta-like site on the network which has reputation.