Having multiple, semisolated compartments in a Hyperloop train is entirely reasonable. There's definitely room in a traincar for the occupants of a compartment that's on fire to move to another compartment for emergency purposes.
Evacuation points would be defined every so often (say every few miles) such that the train could come to an emergency stop within one, seal doors on each side and let air in. This would take a few minutes, but so does landing a plane or stopping a high speed train.
Bottom line is that fire safety is, to me at least, an entirely solvable problem. The biggest problem with Hyperloop, I think, is that given the materials for the vacuum sealed tube and the energy required to hold that vacuum, it is just so unlikely to be more efficient than a maglev. For medium distance travel, even standard high speed rail is good enough to replace planes, so we don't need the extra speed for ~500 mile distances. For longer distances where high speed rail is super slow or impossible, such as across continents and oceans the cost of building the vacuum tube will be so costly that it would take something like a complete ban of non-renewable fuels in aircraft for it to be a consideration. Even then, I think it could end up being cheaper to develop and use renewable fuels for aircraft.