It's not germs people worry about but you don't know how the car seat has Ben handled. Has it been in an accident? How has it been stored? Too hot or too cold can damage the plastic weakening it. Are all the straps in the correct paths and not damaged. Etc.
Exactly. My friend is a certified Child Passenger Safety Technician, and she recommends never renting car seats from a car rental company. There's always a concern about how the seat has been handled, whether it has been in an accident, and what sorts of extreme temperatures it may have been exposed to.
Also, you have to be sure to check the seat expiration date, to make sure the seat isn't expired, as some rental companies don't pay attention to that at all.
She also said a lot of times, rental companies end up not even having a proper seat available for the age of the child, despite the customer having reserved one. So you could end up getting to the rental counter with a rear-facing infant, and being told that all they have available is a forward facing convertible seat, meant for a child much older.
Another thing she mentioned that I hadn't even thought of is that there can be problems in terms of cleaning the seats. The harness webbing on most seats is only supposed to be spot cleaned with a damp cloth, and a very mild soap, at most. They're never supposed to be submerged in water, cleaned with any harsh chemicals, or machine washed. Doing so can damage the integrity of the fibers making up the harness, which can lead to the straps breaking in the event of a crash. Obviously, that's BAD.
When you're talking about rental seats, then you've got pretty much two scenarios: 1) The straps are cleaned per manufacturer recommendations, and are safe, but may not be particularly clean, or 2) The straps are cleaned with chemicals, machine washing, or another prohibited method, and are clean, but unsafe.
Most customers are going to complain if the rental car seat is dirty. They're not going to have a clue though if the seat has been cleaned in a way that compromises the safety of it. So, guess which way the rental companies are likely to go?
Given how much money the rental companies charge for a car seat rental, it's not even worth taking the chance. I can buy my own seat, that I KNOW is safe, for almost the same cost, or sometimes even less.