For instance, in medical terminology, we can tease out the meaning from the words. But I cannot tell why we use 质 for proton and 荷 for charge.
質子 means 有質量的粒子 (subatomic particle with mass, in contrast with electrons which comparably have very little mass), where 質量 means mass (specifically in the field of physics). Although neutrons also have mass, they're called 中子.
荷 generically means load, burden, and in 電荷 it literally means electric load > electric charge.
质 in Chinese mean inseparable (不可分割) such as 质数 （prime number）
Another explaination, 质：事物的根本特性.