Well you have to remember that this was In Panama city Florida. Tyndall is on the coast as such the water table is very high compared to the base.
Basically there is nothing to dig a underground hanger into. And the Renforced aircraft shelters are limited at best in what protection they offer in the modern era it's a why bother. Sure it might survive a near hit but not a direct hit on oh precision weapons render them mute. Finally Continental U.S. is not likely to be taking direct attack with anything smaller then a nuke
The hangers as Jura pointed out elsewhere had ridden out some severe tropical storms before without issue. They were storm proofed to a point. Michael was beyond that. The wind gage at Tyndall broke at 130mph estimates put it at 155mph. This was not a normal storm this was freaking Godzilla. Even as we speak Michael is still causing problems. This was a cat 4 storm that means it was a monster and Tyndell was right at the door when Micheal kicked it down. The base was ground zero. There is no "oh but they coulda..." because Micheal was a destroyer anything in its path is devastated. Micheal is the 4th most powerful storm to hit the U.S. on record. It had the most intense pressure and power of any storm since Camille back in 1969 And wind speed since Andrew. And Tyndell was a direct hit with the most power when it made land fall.