The perspective of cathing a fly that walked on crap five minutes ago disgusts me. I know they cleanse their paws more often than I do mine, but faugh.
2) see the fly walk over your food, your face, your kids food...
Do you want to touch a "dirty" fly, or eat what the fly has walked on?
I'll take #1 any day.
Seriously, we have become irrational animals afraid of everything. (I would wash my hand after splashing a fly if there was a rotten corpse around, though, and would have done even without the fly because my nose would have alerted me of a chemical danger.)
an easy way to catch flies is to put rubbing alcohol in a squirt gun. even less than direct hits takes them out of the sky, and the alcohol cleans stuff in collateral damage.