Why would pilots get special cups?
The answer is pretty simple...

It is because those cups have matching lids that won't fit the passenger cups. Lids are used on the flight deck to keep the liquid inside from spilling on the (ever increasing) electronics, especially those located in the center console between the pilots (which house the radios in a lot of airplanes). 

So some airlines have made a policy of any cup going into the cockpit must have a lid, and these cups specifically have lids.