The key is that Master Pages provide the common content that should be applied to all pages in a site; or at least, all pages that use it. For example, it's very common to require a logo, a menu, etc, on all pages, and a master page is ideal for this; you design the master page with these common elements on them and then every page automatically gets this content too.
A user control is intended for reusable content, wrapping up small bundles of functionality that is to be reused on multiple pages. For example, wrapping a few labels and text boxes (name, address, post code,e tc), which are required on several, but not all pages.
Dave