It didn't count them equally because they weren't allowed to vote. Let's say you had a state with one voter and 9,999,999 people who couldn't vote. Should that guy have the voting power of ten million people?
That guy shouldn't. But do you realize that this flaw exists in today's presidential election system?
If in the entire state of California, only 1 voter casts his ballot and the millions of other don't vote or can't vote, then this single ballot would decide all 55 electoral votes of California.
That's true. The difference is on a percentage basis the people who can't vote today are a tiny percentage of the population. In the antebellum South that wasn't the case.