Possibly trying to keep water out of it so it won't expand and crack.

This is done to keep out the things like leaves and other things that make the fountains dirty. In the spring when the fountains reopen it is not as hard to clean.
This also is done to fountains that have fish in them and the weather is cold. Covering the fountain will help keep the water from freezing over with use of a pump.

Help stop it making hard ice which could damage the decorative surface of the fountains water bowl. Even if empty and in an area of heavy frosts, the frost can still cause damage to some marbles and tiles. We do the same here where it gets down around -10C or 7F in the winter.

If this is in an area that freezes, they are trying to prevent it from cracking, most fountains aren't totally waterproof and the plaster/cement has some water in it, water expands with great strength and can crack cement, frost lifts roads and sidewalks, just frozen water heaving up!

specially in winter most of the plants or small trees as lemon and orange is better to cover with cartoon or plastic bag without broke the roots and leaves
the water fountain is also good idea to cover because sometimes the cold can crack them
some plants are strong are aloes and cactus is not to necessary to cover as the roses are

This is only my opinion but I would have to say it's to keep the snowmen from peeing in them. Of course we don't get snow here except for a five minute flurry every ten years, so I am not an expert on anything that freezes, exept margarita’s...lol. However from the other answers we can derive at a reasonable answer. Honestly, I would go with the freezing and cracking answer, but plastic doesn't seem like a great way to keep concrete or even plaster very warm. So, add to that, the fountain must be drained anyway. That would make covering it to keep it clean, as the pumps and filters could not be in use. And yet that adds the question "Why cover the whole fountain and not just the holding area so that it's beauty would still be seen and appreciated. Enter the maintenance guy who didn't understand what was meant by cover the fountain, or he just had a desire to play with duct tape and waist time. Hopefully they will uncover most of it so it's beauty can be seen, without compromising the safety of its water works. Meanwhile, I am going with a maintenance man/woman who is wrong for the job.