As far as I'm concerned there is no one hard and fast rule, because so much of it is based on factors you can not control. One exception would be if, as one poster above noted, you were thinking about visiting a lot of other Disney resorts during your stay, whether it's to eat at one of their restaurants or partake in some other event or just to stroll or shop. In those instances, it might not be a big deal to use Disney transportation if you're staying at:
A monorail resort, as you're close to the MK bis stops to get to other resorts.
An Epcot resort, as you can boat or walk to the Studios and use their resort buses.
Saratoga Springs, most notably in the Congress Park section, as you're a brief walk to the bus stops at the DTD Marketplace.
Pretty much anywhere else will necessitate a longer trip, as you'll need to bus to a park (or at OKW or Port Orleans, bus to DTD) to get other buses to the resort of choice, and you'll need to factor time accordingly.
After that, it's a combination of timing and personal preferences. On any given day, you could just miss the bus you wanted to take to the park du jour, and wonder how long it would take to wait for another bus versus getting your car, driving over, perhaps braving a wait there for a tram or whether it's early enough that you'll be able to walk to the front gate, etc. And on any given day, you could just go straight to your car, notice the people waiting for a bus, get to the park and see the same people from before ahead of you at the front gate.
Our general rule of thumb seems to be that we prefer taking Disney transportation to MK and driving most other places, especially now that we have one kid and another on the way. We never have to worry about overcrowding, or having to wait for 1 or 2 buses before we can find one with space for us. We don't have to worry about passengers we may find unpleasant. We can listen to the music we want, talk about whatever we want without worrying about being overheard. In the event of a sudden stop and standing room only, a bus can be a little dicey with kids, versus them safely buckled in their car seats (though a bus is probably more likely to sustain less damage in an accident with a car than vice versa). No strollers rolling over our toes, no complaints that the AC is too strong or not strong enough. Far fewer ads for Disney shows and movies above our heads
And when it comes to the ride home, the feeling that we have a LITTLE more control. For example, we can tell when our daughter is about to hit a wall and become too tired to move. If we figure we've got about a half hour, we can anticipate leaving, getting to our car and getting back to our resort without worrying about bus delays or overcrowding taking a cranky tired child and pushing her into a tantrum. And if she does wind up having a tantrum, at least we're not bothering anyone else with it when we're in our own car.