They'll be stuck in a tunnel. Is that worse than being stuck in the desert?
If you're above ground you'd just pop an emergency hatch in the tube.
You can't do that underground.
I'd also point out that a hyperloop tunnel is a much worse place to be stuck in than a normal tunnel.
In a normal tunnel there is room to walk alongside the tracks.
In a hyperloop tunnel there is virtually no room between the car and tunnel - maybe an inch or two, tops.
This also applies to any sort of failure that compromises the vacuum. A dipshit with a rifle could kill anybody in the system in a fraction of a second. Burying the tubes is probably the only way to avoid this, but thankfully the whole thing is vaporware anyway.
Humans can survive (uncomfortably) at .5 atm and you eliminate the vacuum cannon problem simply by putting pressurization valves periodically throughout the tube.
I am not sure what do you mean by 'ubes are not air tight and actually breathe', but they definitely are not air permeable.