USB type-B sockets vs USB Mini-B sockets
Mini-B was popular before the advent of Micro-B. Its downside is the tendency of the plug to get loose, as its relatively small, but doesn't have the hooks that Micro-B has.

So, it's mostly a mechanical thing. Since programmers (I assume you mean EEPROM programmers or something like that) are typically not as size-restricted as say, smartphones, you just use the larger, more durable plug. Makes sense to me. Also, that large plug is easier to handle.