A bit like 'clipless' pedals (disambiguation over here), chamois and their associated creams represent another little nugget of cycling history now frozen in time and taken leave of its context.
The reason the padded part of your cycling shorts has this name is because of Chamois alpine goat, famed for its particularly soft leather - which is is what was used for the padding of cycling shorts before the synthetic materials we use today.
As a natural product, the Chamois leather needed regular treating otherwise it would dry out and crack - that's right, chamois cream wasn't for your skin, but that of your shorts!
Time's moved on, materials have changed - names have stuck - but the anti-chafing and anti-microbial properties of chamois creams have continued to be of benefit. If you're riding long distances, or in particularly wet conditions, both of those qualities come greatly appreciated. And of course, why pay full price if you can grab something on a deal?
