Whether or not perl is an acronym (which has been disputed in this thread and others that I know of), acronyms often get adopted into the language as words unto themselves.

For example, consider SCUBA and LASER. Both words started as acronyms, but by now it's very unusual to see them in all caps. You're a lot more likely to see them as regular words. e.g., "Shoot the scuba gear with the laser (to make unhappy divers)."