It's about being used in the commission of a crime, not that the object committed the crime itself
If I use a payphone to order a hit, is it reasonable for the government to come rip it out of the ground? What if I use a freeway to smuggle drugs? Now the road must be torn out?
Money is fungible and has all sorts of uses. Any particular pile of cash is no more or less likely to be intrinsically criminal in nature. Just like phones and freeways.