My understanding it that larger depositors can ask for a letter of collateraliztion from the bank against assets held by the bank to further cushion the risk of loss. Some banks do and some don't.
If you want that million guaranteed --the answer is yes or have a large, reputable payroll company do it for you. that way they handle all the risk.
Just to give people an idea of how useful bank pronouncements are, here's one from 2 weeks ago by IndyMac: http://www.latimes.com/business/la-fi-indymac1-2008jul01,0,2858219.story "Battling rumors that it may collapse, Pasadena-based IndyMac Bancorp acknowledged Monday that its financial position had deteriorated but described the fears as overblown and said it was working with regulators to improve its "safety and soundness." Lol. P.S. Yeah, it was co-founded by Mozilo in the 80s.
for checking accounts over $100k, you're fubar, but for cd's you can use http://www.cdars.com/index.php the rates also aren't as attractive as if you shopped individually but you get safety and convenience.