What kind of protozoa? What animals are in your collection? Is it in a rack system, aquariums, all in the same enclosure? Natural vivarium? Are they wild-caught or captive bred? How long has this been going on?
Protozoa in general, are spread through fecal/oral contact. The difficult part of protozoa is that they usually have a direct life cycle; that is to say that an affected animal can reinfect itself from it's own stool without the protozoa first passing through another animal.
Some protozoa are more difficult to kill than others. Here's what to do to prevent spreading. Without knowing the answers to the above questions, I'll keep it rather generic.
1: Seperate all animals and keep individually.
2: Simplify all enclosures to paper towel, small plastic hide box and a plastic water dish. Keep all surfaces washer friendly (no wood, rock ect) or replaceable. Don't ignore husbandry requirements of temps and humidity while doing this.
3: See your vet for a disinfectant. I prefer quatsyl, then chlorhexadine, and then bleach if nothing else is available. You vet will help you choose.
4: Treat affected animals as prescribed by your vet. Clean all enclosures daily, spotless. Let the disinfectant soak for 5-20 minutes. (20 ideal, but perhaps not practical for a large collection-see the disinfectant label)
5: All cages should be cleaned seperately, with different utensils (I use paper towels at times like this). At no time should animals come into contact with each other, or into contact with the same equipment. ie, if snakebags are used while cleaning the cage, a different bag should be used for each animal. Buckets should be disinfected inbetween ect.
Have regular stool samples checked for all animals to detect parasitism before it becomes a problem and to measure your success. Esp. with wild-caught animals, a subclinical infection will likely always be present. Healthy animals will be able to keep it in check.
I hope this helps, good luck 
Ian
ps, here's a thamnophis s. parietalis I found a few days ago; hope you enjoy 
