Interesting Thread...
This thread has been particularly interesting for me to read, especially with the variety of opinions being expressed. As most who read this forum are probably aware, I am quite OCD about my own laundry.
If all my clothes could actually take being washed at 60-75º all the time, with lots of detergent and some sort of bleach (oxygen or liquid), then I imagine I wouldn't bother separating my laundry...
Unfortunately, that is not the case, and I'm careful about washing most things hotter than 50º. Darks and lights are separated (Regular clothing, not undergarments/socks), and the undergarments/socks are washed separately again - not because of any particular intestinal trouble, but as a precautionary measure to ensure that clothing of either colour is not "covered" with dirty stuff from down below. I guess if you over-think it, its like keeping hot food hot, and cold food cold; I've separated my Pants/Shirts germs from the ones "down below" (as well as any associated odours or "discolouration"), and maybe, just maybe, the detergent can work that little bit better on whatever germs/stains that remain on the type of load being washed.
Separating my laundry also allows me to use a cycle that fits the type of load - Dark/Denim cycle (lower water level, shorter and more abrasive wash and less interim spinning) for darks, Minimum Iron (higher water level, shorter, gentler wash and some interim spinning) for my Light/Bright shirts/pants and Delicates for Undergarments/Socks (High water level, short, very gentle wash with NO interim spinning and a pulsed slow final spin).
That way, each type of garment gets a more specialised cycle and temperature and can perhaps pre-long the life of some items - especially elastic stuff that would stretch from the bashing and slapping of a lower water level in the Miele FL, delicates in particular in my case (which are also kept suspended in water, with a good detergent dosage, so very good stain/odour removal here. My socks look like new with regular detergent...).
Again, this is just my point of view, and perhaps too OCD - but is good for my clothes more than anything, and is perhaps more sanitary. But, once the Bleach/High Temperature phase of the cycle is over and fresh water is added, you've just introduced whatever lives in your pipes and perhaps your water heater too, just like taking the items out of the machine just re-contaminates them.