Well if it went by congressional district, Democrats would have a much harder time. I'm not in favor of it but the presidential election isn't a popularity contest either. If it's that close and the candidate with less votes comes out on top then it shouldn't matter. Our system was set up like this to prevent the majority from becoming a mob and because our founding fathers didn't think the average voter was sophisticated enough to decide who should be president. The Electoral College is a nice compromise. Only a few times has it not favored the winner of the popular vote.
If the system was set up to prevent the majority from becoming a mob, why would the system be perfectly fine with an arbitrarily geographically entrenched minority becoming a mob?