I hold an Israeli passport, and would like to book a flight with Qatar air, that has a few hours layover in Qatar.
It's that recommend? What would happen if the second flight get delayed, and the airline works want to take me to a hotel over night?
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No matter what, even in the case of delay, you will not be able to enter Qatar with an Israeli passport. If your flight was delayed or cancelled, you'd be stuck in the airport.
That said, transit is allowed for Israeli citizens so you can pass through the airport, you just can't leave it. I'm not sure what would happen if, say, you had a medical emergency, however, and transiting somewhere where there is no way for you to leave the airport under any circumstance is always going to be a risk.
Exactly what the airline will do in the event of a protracted delay will depend on many things. They don't often put passengers in hotels because it's expensive.
In your case you would have to remain in the transit area of the airport unless you have a visa. There is an airside hotel at Hamad International, available only to transit passengers, that the airline might use, or that you could choose to use if they don't offer it.