I'm not sure bugs are the only contaminents they have to worry about. Is a don't-drink order different from a boil-water order? Because if so, tap water probably shouldn't be ingested, boiled or otherwise :)
"Is a don't-drink order different from a boil-water order?"
Don't-drink means contaminants (chemicals, gasoline, etcetera) that render the water unsafe for consumption, period. They're under orders to boil water, as far as I know, which would mean the typical concerns about floodwater contamination... microorganisms and parasites.
It boggles the mind that so many didn't have the common sense to fill up every container they could find with drinking water yesterday.