I find that clecos leave marks on parts. Sometimes it's just a hassle to clean stuff up again after pulling a cleco and putting in a rivet. I was looking at cleco caps, but at $.24 - $.35 each that is just not worth it to me.
So I found "bolt thread protectors" from McMaster Carr -$5 for 100. I just poke a hole in the end - bam! Cleco caps!