Will factory resetting make my rooted device unbootable?

Yes, its safe to do factory reset.

However, I once tried this below approach and bricked my phone. So beware.

If you're using a custom recovery like TWRP and choose complete wipe.

(Advanced wipe -> select all options including Internal, system
,etc)

This erases the complete phone.
So after erase if you do not install a new custom rom immediately (without reboot), your phone goes into infinite loop.

You'll now be stuck with a phone which keeps restarting as no ROM's are available on the phone memory either because of the wipe.

Worst part, My phone didn't have an external SD card so I couldn't copy any other ROM into the phone and to install it later.

My Suggestion : Just be sure of the options you select during Wipe.