Well, I feel your pain, John. A few weeks ago I was cycling into Seattle to get a few days of big city life, which I need occasionally, and noticed a prickly sensation on the back of my right thigh. The hook-and-loop strap on my saddle bag had been sticking out from under the saddle, and its hard nylon edge had rubbed through the short fabric, putting a hole in my own new Pearl Izumi Ultrasensor shorts. Drat!
How to fix? You could just leave it alone. That fabric is remarkably tough and has excellent rip-stop properties, and if you did nothing you d probably find the hole goes unchanged for some time. But it might be best to put some repair tape on it. Stores such as REI carry generic nylon repair tape in various colors, including black, for $3 (rei.com). The stuff would likely last several washings, and if it comes off you just slap another piece on. You could also try McNett Tenacious Tape ($3.50; mcnett.baron-co.com), which seems to have a stronger adhesive than other tapes. It s a clear tape with a matte finish, so it blends well with most fabrics. It should definitely last through a half dozen or so washings.
You might also try an iron-on patch, but use the lowest possible heat setting on the iron to avoid melting the shorts and causing further damage.
And remember that old proverb: Nail that sticks out and tears man s expensive bib shorts, gets snot beaten out of it with large hammer.