From Walter Olson at Overlawyered.com:

It can get tricky when 1) having swine flu may itself count as a protected disability under laws like California’s; 2) innkeepers are required to report communicable disease to authorities; 3) they must nonetheless avoid infringing customers’ privacy; and 4) they can face liability for not taking steps to protect fellow guests and their own workers. And don’t even think of noticing that a new guest is arriving from Mexico…

The relevant quote is from the hotel lawyers blog:

Q:Given all the publicity about the Swine Flu deaths in Mexico, should an innkeeper refuse guests Mexico?

A: The mere fact that there are many cases of Swine Flu in Mexico doesn't mean that everyone traveling from Mexico has the disease. Therefore, no blanket exclusion should be applied. Among other things, it could be argued that such a policy constitutes discrimination based on national origin in violation of both federal and state law.

Another case of Civil Rights Law Doesn't Care If You Die