It’s not so much about the elements, as the molecules. You don’t burn Hydrogen, you burn H2, hydrogen *gas.*
A lot of organic fuels and gas/oil are hydrocarbons, which are oxidized into CO2 and other (often harmful) byproducts. If this CO2 was originally stored in the ground, you are then contributing to overloading the carbon cycle of the atmosphere (plants and animals source its carbon from the air and biosphere, not the deep earth). Hydrogen gas can also be burned/oxidized, but becomes H2O, water.
Additionally, H2 can be refined from both fresh and salt water, which is a near endless source that is restored by *using* said fuel. As a fuel source, one of its big hurdles is that this refining process can be energy intensive, but if you can do it with renewable energy sources (solar/wind/tidal/etc), you can have a clean fuel made cleanly.
Sadly cost is still a big limiter, yeah.
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