It's my understanding that harvesting the gasses is a more complex and involved process than burning them off. The gear and infrastructure is expensive, even if you have something in place for flaring, therefore it normally isn't done for smaller wells.
There's interesting work being done to make some forms of wellhead capture more feasible though.
The challenging is getting the gas from a remote well location to a plant where it can be processed. This requires pipelines, gas gathering facilities, etc. If any of that infrastructure is experiencing an upset condition, the operator has to choose between shutting in the well or flaring the gas. Shutting in the well can be undesirable because it's still producing oil to tanks, and oil is where most of the profit is from. A shut-down well can also be hard to get going again.
Two main reasons AFIK: unstable output (high volume burst but little to no output most of the time) and chemical composition which would require further refining before the gas can be sold.
