How can I tell the lpr command (CUPS) that my file is actually a PDF?
lpr file.pdf
won't print anything.
Answer
Is this really the CUPS-based lpr, or is it a remnant of another spooling system which was not removed before installing CUPS?
Check it by running ldd $(which lpr) and see if there is any reference to libcups.
Also, the complete command should be:
lpr -P printername file.pdf
For a correctly and completely installed CUPS you'd not need to tell it the file type you send to print. It will "auto-type" the input, and apply the right conversion filters to make it digestable by the target printer.