It's def a matter of timing. Q3 was undoubtedly huge - but so was UT, which was the new kid on the block, and it felt a lot more like Q2 than Q3 did.
IMO it was really counterstrike that changed everything - the quake/UT style shooter basically died after CS. UT2004 was the last gasp.
COD4, the game that really hit it big - was basically the next gen of CS. The roots of discontent lie past that point. But between Q3, CS, BF1942 and UT03/04 - the shift to FPS as MP first, SP second was already well underway - and entirely on the PC side. Consoles were probably the only thing keeping single player FPS alive. But that wasn't going to last in the modern, online connected console era - campaigns are simply not the focus of most FPS games nowadays. The blame for that really can't be laid at the feet of consoles and/or a single series. It's just not worth it for anyone to do more than a short, simple, linear campaign when 80% of the reason why people buy your game is MP. Console gamers haven't really taken to 100% MP games....but it hasn't really been tried yet, either.
The real tragedy is that somewhere along the way, the few remaining SP focused FPS devs saw the success of such games, and misattributed it to those simple campaigns. Still, I can't think of too many SP focused, super linear FPSes that were successful, so I dont fully understand the rage. (pun intended)
But MP focused games with short, linear campaigns? Here to stay, and for good reason - the priorities are aligned with what gamers want. All that being said, if someone could figure out how to bring back the UT/Quake style in a modern way, especially in MP....that would be pretty awesome.