Airlines are there to make money so optimized flights are the norm. I can't ever recall an airliner above FL410 (except the Concorde) and even FL410 is pushing it for most airliners.
Some business jets can fly higher because they are certified to higher altitudes but like you said, weight, weather, winds and fuel burn are all part of the equation to accomplish the mission.
Since airlines are looking at cost all the time it is normal for them to optimize their flight patterns (to cut cost and make revenue) where as corporate jets are usually owned by wealthy corporations or individuals that don't require their aircraft to bring in or make money for them. In that sense they can operate their aircrafts (if need be) at less than optimal efficiency and stay at lower altitudes for either comfort reasons like I mentioned before or to cruise at a higher Mach/True airspeed regardless of how much fuel is being burnt out the tail pipes.