First, I think it's a case of momentum. All the scripts are written in shells that are distributed by default in most distros. sh, bash, etc. I write lots of scripts for fish, and I can't convince my co-workers to install fish to run my scripts. They already have bash, they already know bash, etc.

Second, I was recently chided by another fish user for writing fish scripts: "you're using it wrong" was the sentiment. The argument was it's a shell intended to be interactive, but extendable. I don't know how pervasive this line of thinking is, but who's going to learn all about their shell if they're not supposed to write scripts in its language?