Commercial Jets fly the very high for several reasons. First, at
30,000 ft (9000m) the air is thinner, so the aircraft has to push
less out of the way to fly the same speed at a lower altitude where
the air is more dense. Because the aircraft has to push more air to
achieve the desired speed, the engines don't work as hard, also
called "cruising."
The second reason is that up high, the winds are much much
faster, especially in the jet-stream, and a good pilot can use the
winds to his advantage in a tail wind and fly faster and farther
with less fuel. Conversely he can avoid the disadvantage of
headwinds as much as possible by varying his altitude
accordingly.
Thirdly, though the air is much thinner, it usually flows
uniformly and thus the risk of heavy turbulence, often caused by
rising warm air meeting cool air, can be avoided. Pilots who
encounter adverse conditions often issue en-route radio reports to
weather service stations, called "pireps," that give the exact
position, time, and severity of bad conditions like icing or
turbulence.
Lastly, commercial jets travel for long distances, and because
it's efficient to travel at high altitudes, the use "great arcs"
instead of straight lines, to navigate across the (spherical)
surface of the earth. Furthermore, while there are mountains like
the Himalaya's that reach 30,000ft, and there a few species of
birds that fly that high, there really isn't much else up there, so
the danger of hitting something is slim.
Hope I've answered your question.
