Average flu deaths in the U.S. for the last decade are about 35,000 per year. In the U.S., even with vaccines and Omicron, we still had over 70,000 covid deaths in the last 30 days. Given that a typical flu season is 4 to 6 months long, I would say even the last month Covid has been much worse than a typical flu season. So, a covid outbreak in a fallout shelter would still be very difficult in that environment. There will be many older and otherwise immune-compromised people in a crowded shelter who are susceptible to a still highly contagious virus. It is completely reasonable to at least attempt to be cautious in the short term.

By the way, "everyone" is not vaccinated. Only 65% of Americans are fully immunized at this point. I'm not saying Covid is the threat it was a year ago, but some prudence is still reasonable.