Loading different denominations into an ATM in the US is a matter of programming as the bills are the same size, no matter the denomination. Most ATM have 4-6 cassettes in which the bills are loaded; you just program the machine to know what denominations are in the cassettes.
At a certain point, when a cassette is low, it needs to be replenished. This is normally done with two custodians (dual control) and most banks do not have extra FTE do be doing this numerous times during the day. It makes it much easier and efficient to stock the same denomination in all cassettes and let the all the cassettes run low before replenishing, rather than having to service the machine every time it runs out of a denomination.
That being said, a number of banks do have multi denominational ATM machnes out there; some even have coin dispensers as well.
For those with OMNI access, please see:
http://flyertalk.com/forum/showthread.php?t=704539