Open-coil humbucking pickups have the coils wound around plastic bobbins, which are usually black, cream, white, or any number of colours. You cannot easily (and permanently) change the colour of the bobbins on a humbucker.
Single-coil pickups (strat-type) get their colour from a plastic cover that encases the whole pickup, with the exception of the pole pieces, which protrude through the top.
On a humbucking pickup, bobbin toppers just cover the top of the bobbin (duh) and leave the pole pieces and coils exposed. A bobbin topper on a single coil just goes over the top part of the existing plastic pickup cover.
Pickup covers on a humbucker are usually metal, usually cover at least one row of pole pieces, and are usually soldered to the pickup's base plate to give improved shielding and grounding. They also affect the pickup's tone slightly.
Single coil (strat-style) pickup covers are usually just plastic, and can be swapped out if you want different coloured pickups.