Wash your shorts regularly (after each ride or day's commute) to prevent infections and saddle sores.
Hang dry the shorts to eliminate mechanical wear from the dryer and the potential for damage to the elastic fibers caused by high heat.
When hang drying, do so in the shade, to reduce fading and damage done by direct sunlight.
Avoid fabric softeners - they interfere with the wicking ability of the fabrics.
Consider using a dye and fragrance-free detergent to avoid the build-up of unnecessary chemicals in the fabric.
Be careful when applying insect repellants containing DEET, which can damage plastics and synthetic fabrics.
Inspect your seat-post bolt(s) to make sure they don't have any protruding or sharp edges that can tear holes in your shorts.
Inspect any Velcro, zip-tie or other fasteners on your saddle, seat-pack and top tube to make sure that they can't snag or rub against your shorts.
Avoid jackets, jerseys, and vests with Velcro at the hemline that could rub against your shorts while pedaling or walking. Velcro will very rapidly chew through the Lycra fabric used in bike shorts.
Place gloves and other clothing with Velcro on it in a separate "delicates" mesh bag in the laundry, to keep the Velcro from snagging the Lycra fabrics during the wash cycle.