I do apply a good linement after the post-ride vet exam because I think it 
makes the horse feel better.
For trailering I changed to using light shipping boots with velcro 
closures.  This provided protection against scrapes and abrasions without 
pressure on his legs, and they could be easily removed at rest stops to let 
his legs cool.  On short hauls I often left his legs bare.
Kahlil completed his last 10,000 miles or so without having his legs 
wrapped, not to mention tens of thousands of miles in the trailer with only 
light shipping boots (or nothing).  He suffered no ill effects from this 
and to this day his legs look remarkably clean.