Yeah, it was the system insisting that I should take BART, even on Monday. Technically, it seems to be slightly faster to take the VTA 60 bus to Milpitas BART and then BART to San Francisco. But this isn't the route I want, so I had to put it together by individual pieces, as I know they should work:

VTA Karina Station to SJ Diridon Station
Caltrain SJ Diridon to SF 4th & King
Muni T line to Union Square then 38R bus to Geary & Laguna