Water based Primer??

Kingston,

You don't have to prime them if you don't want to. Priming is usually done on parts that need the paint to adhere better so that it will handle masking, etc better. If those mud flaps are not going to be masked or anything then you could just shoot them with the color you are painting them and they should come out good. If the color is fairly light it may need two coats or you could just use a primer first to give you a flat gray finish to start with.
Model Master has a primer in their Acryl line if you have to have water based.
I prefer solvent based for primers as they bite into the surface better and create a stronger bond to the material. I use only one primer and that is Floquil primer from their railroad line of colors. It is an enamel based paint and I thin it with mineral spirits.

Mike

I secound what Mike says. If you are going to prime go to Wal mart and get a can of omaga Sanding Primer gray for $1.78 and it will last a long time.