You've mishead; it's not hydrogen, it's nitrogen that is dominant in the atmosphere, which means that the nitrogren and oxygen components are quite similar to Earth (78.09% nitrogen, 20.95% oxygen).
The stated reason in the movie for why humans can't breathe is the high carbon dioxide content, which at over 3% is significantly higher than that of Earth (0.039%, so it's almost 100 times higher):
Janek: What is the atmosphere?
Ravel: Atmosphere is 71 percent nitrogen, 21 percent oxygen, traces of argon gas.
Janek: Whoa, now, that's weather.
Charlie Holloway: Just like home.
Ford: Only if you're breathing through an exhaust pipe. CO2 is over 3 percent. Two minutes without a suit, you're dead.
The Engineers obviously therefore breathe a similar nitrogen/oxygen mix to that which we do, but have higher tolerance for carbon dioxide.
On an interesting sidenote, and as noted in this question, carbon dioxide in the movie is an obvious error: carbon dioxide in that concentration is not so poisonous, and nor is it in any event produced by an exhaust; carbon monoxide is what it obviously should be.
That the Engineers might have a biological requirement for breathing such a high level of carbon monoxide (or dioxide) may be discounted. The atmosphere inside their ship was breathable by humans (as the scene in the control room - where the humans are without their helmets - confirms), so evidently their preferred atmosphere mix is something that is breathable by humans, i.e non-lethal to us. However, the surviving Engineer apparently made it from his ship to the lifeboat without a helmet, so they appear to have a higher tolerance for a mixture that would be fatal to humans.