Hi,
Well it is also a matter of stock space and functionality. The LM339 can be used for more things, and if you dont need the full function of the 555 anyway then you can use the LM339 without much more difficulty.
For example, in the typical clock oscillator the 555 might require 2 resistors and two caps, while the LM339 oscillator requires 4 resistors and one cap, but while then the 555 is "all used up", the LM339 still has three more sections not used yet that can be used for something else that probably really needs a comparator too like under/over voltage detection.
The frequency stability of the 555 is very very good too but it's not due to any special design of the chip active components, it's because of the internal connections of the resistors. That means we can build an oscillator that should have frequency stability just as good with an LM339 if we set it up almost the same. It turns out that it works pretty good because the two oscillators are wired almost the same.
One advantage the 555 has over the LM339 is the output drive capability is much better for the 555. The LM339 needs a small driver transistor to drive 100ma loads. I guess the main advantage of the LM339 is that you get four sections to work with instead of just one or two with the dual version of the 555.
The question is what to stock. Stocking both requires more space and more inventory complexity, so decisions are made based on price and flexibility of that part to fit into other circuits.