It wasn't set up to protect the voters equally, but more for each state to be more equal, and more to the point to give more power to southern states that had less large cities but much more slaves. The electoral college and the 3/5's compromise both stem from the debates of how to apportion representation. So now we have a system where a voter in Wyoming counts 3.6 times one in California, hardly equal.
Another reason for the Electoral college was the distance & time it took to get information from one part of the country to another. So instead of direct representation, the citizens voted for a slate of presumably more informed electors who were up on the current events and issues of the time. In addition this was also thought to be a good protection against the voters being swayed by a snake oil salesmen promising them magic beans. While we can debate how well informed today's voters are, we can't debate that the tools to inform one's self are out there and readily available to anyone who wants to make use of them.
The argument that rural voters in small and Midwestern states would be meaningless or that one party would be in total control is completely specious. Our government is set up in 3 branches, and today, yes the executive branch would have been Dem more often under a direct vote system, but that would still be checked by the House/Senate. And a true check & balance system vs the current system where the executive branch has assumed more and more power that is rubber stamped by the house is a lot closer to what the Founding Fathers had in mind.
Finally, IMO, the current winner take all system discourages 3rd/multiple party systems which I have seen a fair number of people here support. Reasons stated better than me here and here.