I've never bought one and am glad because it would have been a waste of money. When they're small you can just pop a muslin wrap or terry cloth or some other cheap fabric over those red cradle type carriers in trolleys. When they're a bit older and you decide to put them in the actual handlebar section, you can just use an anti bacterial wipe or baby wipe to wipe down the areas you think will be touched/licked by them.
The other option, like you mentioned, is to just carry them in a sling. I have an ergo but I got the Suppori sling recently and it's been great for those short shopping trips where I don't need a trolley, very quick and easy to get him into and out of it.