Sit on the saddle while riding, straddle the top bar while standing. You should not expect to be able to stand on the ground while seated on a conventional bicycle that fits you properly. Concern yourself with the distance of the saddle from the pedals, not the ground.

You want to have your leg almost straight at the bottom of the pedal stroke.

Check out the Electra Townie featuring "flat foot technology" if you want to remain seated at stops.