The syntax is similar, so you may be able to compile some code snippets. JavaScript looks more like the old Actionscript 2 though.
It's not only jQuery, but most JavaScript libraries are used to interact with the user interface or doing some communication things in the background. If they weren't, you could probably replace them with a server side library for the same job.
Many APIs, like the ones used for input and output are very different. If you are thinking of a copy&paste approach to convert a library, you would need to recreate a lot of those APIs for it to work. For example, a library to draw something on a canvas: You would either need to recreate the canvas API to draw the canvas instructions in flash - or create a wrapper to make flash call the original API to draw it on a real canvas. Alternatively rewrite all those parts, which are likely to found almost everywhere in the library.
That leaves us with libraries that strictly use non-js specific stuff. Maybe encoding/decoding libraries or algorithm and math heavy libraries. Those libraries may can be converted more easily. It would be quite a lot of work to refactor them into maintainable code though (in the OOP based Actionscript 3 sense). Apart from some less changes in the syntax, it probably requires almost the same amount of work to port the library to any other language. Also, chances are, that those generic libraries already exist for Actionscript.