We run into this sort of stuff all of the time in the reptile trade...how turtles carry saelmonella, that you can catch herptoencephalitis from garter snakes, etc...
The facts are clear: if you do anything but stay in a "clean room" for the rest of your life, you do run the risk of catching a myriad of diseases...we are going through a wonderful West Nile Virus panic attack right now in Arizona...people get bitten by a mosquito and head for the emergency room! It is true that bringing in animals to your house may increase the chance of getting an exotic infection...personally, I would just stick with trying to be healthy and a little careful, and not freaking out about it.
Of course, that IS how I caught Malaria!
I have to confess sticking my hand into the tank when I knew I had a small cut on my finger, and I knew I shouldn't be doing that. As a result, I got a finger infection and had to go through two rounds of antibiotics.
However, I did recently read that we shouldn't be very worried about aquariums as health hazards, because the animals are too different from us and don't transmit their diseases to us.
Of course, we DO work with some other sources of nasty stuff. Consider all the critters we might own. Some urchins (and starfish!) are capable of exposing you to some unpleasant toxins. Cnidarians of various sorts are potentially dangerous--I have a potentially very painful coral (the consequence of impulse-buying a pretty critter without researching it first.... )
And even if you aren't into corals or such, consider the live rock you buy--quite possible you have some fireworms or other hitchikers. Some Zoanthids hitchiked on my live rock and were VERY happy in their new home, multiplying quickly. I've never confirmed the genus, but I'm 90% sure they're of the type that produces palytoxin, a very serious neurotoxin stored in their mucus (NOT in their stinging cells.) A coincidental accident removed most of them from my tank, happily. I just don't like having something that could hurt me badly in there.
Anyway...I agree, rubber gloves and careful hygeine are probably a very wise course of action. I use them all the time now. Of course, what I REALLY want is decent elbow-length disposable gloves, but I haven't found any yet...
Valid points! So much about marine life is so mysterious to us...it's funny what kind of dangerous critters are commonly offered in the same pet shops that can't sell rattlesnakes and gila monsters.
Rusty and anyone who would rather be safe than sorry...these are the gloves I use. I can just barely clean the substrate of my 90 gallon tank without getting my hands, elbows and upper arms wet. for 13 bucks they rock. http://www.thatpetplace.com/ Do a search for "Aqua Gloves 28" I'd link right to it, but the addressing seems complicated.