Why will a baseball go farther then a softball when you throw it?

An object with less mass will have a greater speed when the same amount of energy is expended into it. Thus, a Baseball will be going much faster than a softball at the time it is thrown. For the same angle of launch, an object will go further when it has a higher velocity (a fairly trivial and simple fact).

Additionally, an object with greater surface area is slowed much quicker than one with less surface area. The baseball experiences less drag at the same speed than the softabll; while it is travelling faster and experiences greater drag as a result, it will also go further before being remotely near to the speed of the softball.