I am one of those Vet nurses who run puppy preschools at a vet clinic. I have completed my dog trainers course and train at other centres. Please don't assume that all Vet Clinics have trainers that aren't qualified. Definately ask the clinic before attending though because I do agree that a bad trainer can destroy your dog for life.
Puppies are 90% vaccinated after their 2nd vaccination, so the risk of them contracting diseases is very small. I wouldn't recommended taking a puppy to a clinic for puppy school if the clinic has had recent cases of Parvo through it. With that said, once the clinic have cleaned every surface properly with the disinfectants they use for various diseases, then it is safe to return.
It's a proven fact that the critical period of socailisation for a dog is between the ages of 8 -16 weeks thereabouts. So if you wait until your puppy is fully vaccinated before socailising them, you miss that small window of opportunity. I have run Puppy school classes for 5 years now and have never had a puppy contract any diseases.
The clinic where I run it don't make a cent for puppy school as they employ me to do it, so it isn't a money making scheme for all clinics. They like to have classes run there so the dog actually enjoys coming to the clinic rather than needing to be dragged in by there owners.
Everyone owner needs to make the decision between early socialisation for their pup or isolation for the risk of contracting a disease, but from my experience, there isn't much of a risk.