IMHO most of the wear & tear on the cockpit covers occurs while you're travelling down the open road.  After a while the cover looks like a flag that has blown in the wind too long.  One solution for that would be to build a stripper cockpit cover.  Take some cedar strips, fashion them to fit across a cockpit, glue fair, glass, varnish , etc.  Make an L-shaped lip on the front to grab a lot of the front of your keyhole.  Add a stub at the back edge to lock the cover in place.  Leave enough room under the lip at the front to put a thin layer of foam or something to keep the cover from rubbing the finish off your cockpit coaming.  You can finish it bright, paint it to match your truck, or cover it with a fabric or neo cover.  But always strap it down (snug, not tight) when travelling.  Makes an easy winter project.  Have fun and keep paddling.

I made my own neoprene cockpit cover for my Shearwater 14.  It was quite easy.  All you need is a piece of neoprene (you can choose the thickness - I think I used 2 or 3 mm, nylon on both sides), a length of bungee and some neoprene glue. I got the neoprene and glue from Seattle Fabrics (http://www.seattlefabrics.com/products.html)  They have a wide selection of colors.

Place the neoprene over the cockpit with the "inside" side up (I used some of those ubiquitous clamps from building to hold it in place temporarily, or an extra set of hands would work too).  Stretch the bungee cord around the cockpit under the rim (on top of the neoprene).  Tie it off in the front of the cockpit.  Stretch the neoprene so it's as tight as you want it.  Then trim the neoprene leaving about 1"on the outside of the bungee.  This 1" flap of neoprene will fold up over the bungee and make a sleeve with the bungee inside.  You need to cut a little v-shaped section out of the front of the flap so that the knot in the bungee cord can stick through.  Coat this 1" flap with neoprene cement as well as the part of the cover it will fold up and stick to.  Let dry and recoat according to the directions on the glue bottle.  Fold the flap up, let it set to cure, and you've got the cover (upside down, flip it over for finished product).  

I left enough bungee sticking out the front of the cover so that I could tie it to my deck rigging (just in case it comes off when on top of the car for some reason).  You could also put a little plastic clip on it to make it easier to attach/detach.  

If you are going to use the covers as heavily as you mentioned, you could also sew the edge of the sleeve to re-inforce the glue seam.  However, you need a really heavy duty sewing machine with a good needle to do this (there are places, like Seattle Fabric, that have commercial machines that can sew neoprene for a nominal fee)

I sewed my from rubber backed canvas, bought at fabricland.  made a pattern form the cockpit rim with 1/2" extra.  I then cut a strip of fabric about 2" wide.  That was folded over and sewed to the edge, 1/2" in.  I then strung bunjee cord through the tube. 

Since I was using a left over piece of bunjee, I made it shorter than I would have chosen to use but I am REALLY happy with the result.  I sewed three of them, one for my boat, one for my wife's WD12 and one for my nephew's boat.

2 seasons later and one 2,400KM trip and it has not budged an inch and 100% waterproof.  Also, don't forget to sew a webbing loop so that you can attach the cover just in case it does come loose.