The U.S. CDC (Center for Disease Control) really started looking at this mass "prophylaxis" (protection) immediately after the anthrax scare of 2001. One of the issues they know they had to overcome was moving this large number of people through long lines and still maintain control. It dawned upon them that there was one industry in the private sector that does this, and does it well enough to make money. CDC planners began visiting operators of the large amusement parks in the country to find the secret of handling large number of people. They are now incorporating these lessons learned into plans to deal with a biological weapon release if needed.
The worst case scenario for terrorist use of a biological warfare is the wide spread release of something in a large population area. While four of the five most dangerous bugs are easily treated with off the shelf antibiotics and the fifth, smallpox, is also easily treated with vaccinations, treating a large population (a million people or more) is a difficult problem. Medical experts in this field consider that local governments will have about 100 hours from first detection of disease, to completing the treatment without suffering large scale fatalities.