It disambiguates labels from registers, assuming of course you allow labels to have register names. eg this is valid:

        mov rax,%rax                                                            
  rax:  .ascii "hello\0"

Stupid perhaps, but valid.

I wonder if it would have been more ergonomic to have the labels be % prefixed instead of registers.

The above-linked article specifically points out that registers are referenced much more often than labels.

Probably an artifact of the original use of the assembler being to process compiler output, and causing variable names to appear.

Yep, the "nice" thing about AT&T is that, from a parsing perspective, you don't really need to know much about the target architecture to be able to determine what's an instruction vs. a register vs. a label, etc.