Abundance. While Hydrogen must be extracted from water here on earth, in space it is the most abundant element. Stars are made of it, nebula contain a lot of it, and there are interstellar gas clouds that are mostly hydrogen. Combine that with how energetic a fuel it is, and the reason it’s used is obvious.
An example: in the game Elite Dangerous, the primary energy source on your ship is a fusion reactor. Naturally, the fuel for the fusion reaction is hydrogen, and so to refuel your ship, you fly through a stars corona and collect the hydrogen gas from it. And yes, overheating your ship is a concern during these refueling operations, especially if they take too long.
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