I always used a cover (which I made) for ds when he was a little munchkin.
But, not so much because of germ fears (I was never too rabid about that).
Using a cover was about comfort!!
The cover I made was of soft fabric (imprinted with poison-dart frogs in bright colours), and had extra padding (memory foam) in the seat and a wide band (lined with flannel) that had velcro around the back. It held him in place beautifully and comfortably (without propping things around him to hold him up!). He couldn't reach the velcro, so no worries about his trying to climb out (he never tried to undo it anyway). The cart handle was also covered and that made it more comfortable for me, as well (he never gnawed on it). I had loops on it to hold a little toy for him to play with as well as a small plastic mirror (though he generally preferred to look around and listen to me talk to him about things!).
The carts were often cold/freezing in the Winter, wet after a rain and hot in the Summer. I never wanted him to be uncomfortable while we shopped. I think the cover made it so nice for him.
I often made these as gifts for new Moms we knew and I saw them used everytime I met them in the stores. I just bought fabric to make one for my doctor's daughter (she is also a doctor and loves Mothering!) to use for her baby (now 7 months old).