Gmail labels are different than folders, in that a message (or conversation) can have multiple labels. Generally speaking a message can only exist in one "folder".

It's easy to simulate labels as folders, however. Just make sure a message only ever has one label. "Inbox" is a special label in Gmail, but it's still just a label.

To do this automatically, when you create your filter to move the message to the label(s) you want, also check "Skip the Inbox". Then new messages that meet your filter criteria will not be in the Inbox.