This is a really good question and you've received mostly crap answers. "Testosterone" isn't an answer although it may be part of an answer. "Stronger" muscle isn't an answer although it might be part of one. My speculations are for distance running and not sprints.
1. reducing swing weight of lower limbs will lower the amount of energy necessary to run since a smaller mass will be accelerating. Lower bone density, less tendon/ligament mass, less fat mass, and less muscle mass would all contribute to swing weight. Since we need at least some muscle to swing the leg there is obviously a trade-off between too little and too much muscle and this will of course depend. If testosterone builds muscle mass/bone mass etc (along with GH and other hormones) then more will not always be better. Other than fat mass, this would suggest women should run faster.
2. The body itself will accelerate up/down and back/forth and the less mass in the trunk/upper limbs/head the less energy needed for this waisted energy.
3. gearing. males have longer bones as they grow for a longer period of time. Without giving it any though beyond what I'm vesuviating here, longer bones should make longer output levers which should increase kinematic (velocity advantage). Maybe this increases power. Longer bones also mean longer muscles which will increase relative shortening velocity and thus power. On the other hand longer limbs could reduce power by decreasing the mechanical advantage but maybe this is offset by the added muscle and increased relative velocity. Of course taller males are not particularly good at distance running but maybe this isn't because of long limbs but because of heat retention so the negative correlation between limb length and running ability is spurious and not causal (and the actual causal pattern is positive).
4. Hip angle and valgus knee in females (due to the wide hips). I have no idea how this effects running speed/efficiency but if their weren't biomechanical maladaptations to this I suspect we'd all have wider hips (driven by selection for bigger heads).
5. added body mass due to excess fat tissue has at least one other affect other than increased cost to acceleration and that is a decreased ability to shed heat.
6. Someone has probably developed a mechanical model with all this and found the optima.
I would speculate that the percent body fat explains a sizeable portion of the difference. Elite lady runners have noticeably little body fat, which isn't true of nordic skiers and swimmers (cylers?). So clearly glide phases in skiing, and swimming (cycling?) make excess fat less costly (and maybe actually be favorable as they would increase flotation in swimming and downhill speed in skiing.
Many people answered "strength" but the answer is much more than strength. Certainly many women will have more leg muscle mass than elite runners so if it were just strength, they should be running faster.