KQED pays NPR for NPR produced shows that KQED chooses to air. So, yes NPR gets some of that money indirectly. I believe it is possible to support NPR directly via their website.

I sort of do this already with my local public broadcaster. I give to OPB but I also make a separate donation to KMHD radio because I value what they are doing. The money all ends up under the same umbrella organization but I hope the separate stream shows that their listeners value this relatively small part of the overall mission.