It is worthwhile to protect electronics with a 3D printed PLA case?

As pointed out by Ryan Carlyle, not all 3D printing filament is flammable (such as PET and PETG), and the question therefore rather becomes:

Can 3D printing be used to make proper electronic cases?

And the short answer to that is yes. 3D printing allows to make customized cases of all varieties. Also, since there is huge variety of materials available, you not only restricted to cases of plastic filaments - should this be of interest.

Then again, it all depends on what you are protecting your electronics from. If you plan on submerging your electronics into water or throw them into a fire, 3D printing might not work for you at all. If dust protection is your only concern, however, 3D printed cases should do just fine in most cases.

It depends.

Protecting your electronics from being touched by random bits of conductive material which would short and fry them is always a good idea.

If it's something that will be visible, then a pleasant printed casing might go well. You might just as well use any other casing though, there's no requirement it be 3D printed.

For a very small circuitboard (an inch or less) heatshrink tubing might be a better form of protection. Or just insulating tape.

If you never intend to access the circuitry again and heat dissipation isn't a big issue, then just putting the whole lot in potting compound may work best for you - complete waterproofing and environmental protection.

Or you could just tape a bit of plastic from a 2l coke bottle over it, and get 99% of the protection you'll ever need, and still keep the circuit visible and accessible.

Ultimately, it boils down to: Do you want it to be covered? If so, by what? If you would prefer a 3D printed case, then do you want it enough that it is worth the time and effort to you?