Why is kapitan in nomative and not instrumental? I though jest makes it instrumental.
Ehm... This sentence is quite different from e.g. "Michael is a captain", isn't it? You just tried to define 'where' by saying that it is a captain ;)
Look at it from the other side and answer it: "Kapitan jest tutaj." The captain is clearly the subject of the sentence. And so is the situation with the question as well.
Ahh yes ofc.. Dziękuję bardzo Jellei. Trying hard to remember all those grammar rules.
Don't worry, people often spread some rules too far. A lot of learners have moments when they try to use Instrumental after absolutely any "jest".
Just a reminder, for example "Kapitan jest wysoki" (The captain is tall) also doesn't take Instrumental, because only noun phrases take it, and here we just have an adjective.