I would say human error or misjudgement combined with other factors like weather or mechanical failures. This can be further contributed by financial pressures to meet schedules and hold down costs from delays.
As to weather, past experiences, improved technology to sense potential high risk weather (including microbursts, downdrafts, unusual winds) is reducing in many locations those risks. However, as we recently seen in the AF
crash landing in Toronto and in Peru with the TAMS crash, having insufficient information about or misjudging weather conditions probably were added factors of those crashes.
As to mechanical, the Helios crash in Greece is probably due to a series of mechanical failures, (depressurization failure combined with a possible faulty emergency O2 system for the cockpit) but also possible misjudgment by the co-pilot to drop the a/c to a safe level more quickly. The AA
587 crash of Nov. 12, 2001 is hotly debated here as to causes including structural failure, rudder control design issues by Airbus, poor judgment of pilots in operating the rudder perhaps due to training errors, combined with wake turbulance from a 747 that had taken off just before it.
As noted above, poor judgment of pilots can be in a number of ways. About 6-7 years ago, a FedEx DC-10 arriving at EWR
crashed upon landing and became a write off (crew survived). This was at the end of a long overnight flight, so one has to consider being tired, jet lagged and related factors causing an hard or crash landing. The NW
crash at DTW
a number of years ago was due to improper flap settings by the pilot. The KAL 007 flight disaster has a high probability of improper settings of the autopilot and the failure of he pilots to notice or correct their error.
Failure of pilots or inexperience with a particular a/c or airport can also add to the problem. In February, when a bizjet crashed at Teterboro airport, questions were raised about the balance and overall weight on the a/c, something that should have been the responsibility of the pilot/co-pilot.
Lack of knowlege of and general inexperience dealing with hazy conditions probably led to the crash by John F. Kennedy, Jr. in his a/c.
Mechanical failures or weather rarely itself causes a crash, but since humans are behind the stick or yoke, then you will have that as a factor.