New nodes inherit permissions from the site nodes they are created with. If you go the the main site site map and create folders and subfolders they will all inherit from the main site. If you create subsite1 and go to it's admin/site-map page and create subfolder they will inherit from that subsite.
It would be nice to build into the site map interface the ability to pick what node to inherit from. Sometimes it's better to use the node above you instead of the subsite you are in.
