You really shouldn't get that many germs from the patient back into the CPAP machine, since they'd have to "swim" upstream in the air flow. Also, other than the water tank, it's not a very good germ growth environment, since it's dry. Maybe they're a little afraid of germs from the hospital room getting into the machine and lurking there.
In any case, I think the antibacterial filters are mostly for lawsuit/CYA/yuck factor/abundance of caution reasons.
I also think they're intended for single night use. If you have a humidifier, the filter is going to be a dust coated, warm, wet sponge. If you don't throw it away after a night or two worth of use, it sounds to me like it will be a germ breeding ground. Would you breathe through a wet rag one and then keep breathing through the same rag night after night without cleaning?