Yes: you can just rename the .cdr file to an .iso. It's the same container format.
No. Handbrake doesn't mount .iso files. You need another utility to mount on a PC. On a Mac, just double click it to mount.
Once it's mounted, you can feed it to Handbrake.
If you ripped it to a .cdr file, you were presumably using Disk Utility on a Mac. If there were copy protection, the rip would have failed.
Unless you were using Fairmount with Disk Utility to rip a copy protected DVD. But you'd know if you'd done that. Unless you were really wasted or something. (I got drunk in February, reactivated my Star Trek Online account as F2P, and completed every mission and quest they'd added since launch. I barely remember any of it.)
Why all the winky winky?