Could you just use .gitignore so folders you do not want included do not get committed to git repo? If not from what I understand, if you are using a workspace, the first folder needs to be the one with the cursor rules. as thats the only one that will get picked up, so maybe make sure the folder is first and also alphabetically first (not sure if that also matters). But if you could just do gitignore you would be better off.
I have another idea but not sure I need to test it - some .cursor files seem to be allowed in the user directory (such as .cursor/mcp.json) - I dont think its supported, but you could try to put rules in their and see if the get picked up.
If not, this would be a great feature add by cursor.