Rubber retains some flexibility so can be repaired, have small changes made, etc. Vinyl hardens up pretty quickly and tends to fall apart when removed. I can't say that it's ever seemed like a big deal, though.
I believe that rubber is considered an upgrade, and costs a little more. 95% of jobs spec vinyl though. LEED projects though will often spec rubber because it is a natural product and requires less energy to produce.
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