I think it works very well. With Endurance, Athletics and Acrobatics, just about any possible physical activity is covered with a skill. This means that there is no debate about whether any kind of out-of-combat physical activity would be a skill check or not. If you need to do some kind of extraordinary physical feat of any kind, make a skill check.
Along with the basic idea of using Endurance to simply out-run something (which seems like it would come up often enough for PCs), there are a few other things it can be used for that I can think of.
You need to make an Endurance check to hold your breath in case of water or poison gas.
You need to make an Endurance check in order to withstand harsh travel conditions (like travel through extreme hot or cold).
You may need an Endurance check to hold on for dear life to the handrail of an airship falling out of the sky, or the back of a dragon trying to throw you off. Holding on to a plank of wood while floating through storm-tossed seas or holding on to a rock to avoid being swept away by a flood are related uses of the skill.
While I imagine Athletics would be used if you want to throw something, you want Endurance if you want to carry something heavy as part of a skill challenge.
At truly epic levels, you need to use Endurance to hold the sky up while Atlas takes a break.