When I type
lsusb I can see the USB is showing as connected to Canon. However when I do
lpr print.pdf it doesn't print anything at all.
How can I fix it so that I can print using the command
I would try to use CUPS to manage printer, driver and documents, if something wrong continues to happend, so you would investigate for specific problems (such as printer device, printer driver, or even if your linux is sending the correct parameters for your printer).
I hope CUPS will solve your problem. Good look, and dot forget to post yor results here :D