My base ideology is libertarian, so I'm all for individual freedoms. I honestly believe that, in the vast majority of cases, a system that emphasizes strong individual freedom and personal responsibility will leave humanity better off.
With that said, all ideologies eventually smack into reality, and none to date deal with it perfectly. One of these realities are germs. Disease does not respect the individual model and demands a coordinated approach. Absent a 100% safe and effective vaccine (which would be compatible with individualism), the only way to stomp out a communicable disease is to reduce the population with it to such a degree that it fizzles out.
As such, I feel that we can and should make allowances for individuals to act selfishly or in ignorance, but only up to the point where the vaccines are no longer effective in wiping out the diseases. At that point, you have to make the pragmatic decision to set your failed ideology to the side for the moment and solve the problem at hand.