In Science we use a set of units called the Standard International Units. The kilogram, the meter, the second, the ampere, the mole, the Kelvin and the candela. All of our other measurements are taken by combining and defining these units. But in quantum mechanics we use a set of units called the planck units. There's a planck distance, a planck time, even a planck energy, mass and so on. The planck units are based on actual physical features of the universe. The planck distance for instance is the smallest distance across which the laws of physics are known to definitely work (anything smaller and we don't know). So why not switch to these units, why keep the SI ones?
The answer is mainly historical. In 1875 a meeting of Scientists took place to agree on International units to use, and it was called "The Meter Convention". It was here that they decided on the meter as the unit of measurement, the kilogram as a unit of mass and so on. They got their units largely from measuring the Earth and doing calculations on it. There is, in fact, an original kilogram made of platinum sitting in a vault at the Pavillon de Breteuil, likewise an original meter. The current SI units were largely decided at a meetings between 1875 and 1960, but the General Conference of Weights and Measures still meets every few years to review things.
While the planck system of units is, in a sense, a more fundamental property of the universe, the reason the GCWM use the current system is because it must be used by all Scientists all over the world, not just quantum Scientists. Furthermore, the quantum system is a lot newer and less familiar to people.
For me, the only SI unit which actually bugs me is the unit of ampere to measure electrical current. Because an ampere is a coulomb per second, I personally would have made a coulomb the fundamental unit of charge and made ampere the derived unit. But there are more people in the world who deal in current than actually deal with the property of charge itself, so the ampere sticks. So the reason we use the scales we do is mainly out of international agreement and "what's best for everyone to communicate" rather than "what's the Universe fundamentally doing". I can see arguments for both ways of doing things.