BMX bikes have very low seats (or no seats for some models) because BMX racing is an out-of-the-seat, balls-to-the-wall sprint for maybe a couple hundred yards at the most, or they're used for freestyle or trials riding where you're out of the saddle and balancing on the pedals anyway. They're not really intended for commuting or distance riding, they're special bikes for a special type of racing.
You only have so many standing pedal strokes in your system per day, so what you're doing is really an inefficient way to ride. Learn to use your saddle and use your gears -- one of the LAB cycling courses might be a good idea -- and your body will thank you for it.