Only allow files to be read, no permissions to write, copy or delete

You could just set a document to read-only. This will completely disable the ability to edit the document and you can do it when you save the document, no external apps required.

There is a need to differentiate between protecting the contents of the document and pretecting the file at file system level.

To protect the contents of a document, it depend on the format, MS office documents can be protected on different levels, open, modify etc. This does mean the content.

However to protect a file in the file system, the file system itself would have to provide rights management for it. One set the archive or write protect bit also on the file, but this is in fact just a kind of flag, this can be removed again.

Problem with usb drives might be that when they are formated as FAT32, there is no real rights management existing at file system level.
If someone needs to use NTFS, which would support rights management, then this is applicable to certain user or user group and this will work only with the proper windows management also connected, means on that particular computer where those users or groups are set up and such usb drive will therefore notbe portable any more.