Intentions matter more so than just raw numbers. If you kill 10 people by accident, even negligence, that is generally considered as not being as bad as killing one person on purpose. The vast majority of deaths attributed to communist regimes come from incompetence and mismanagement resulting in mass famines.
Furthermore, the reason the Nazis are so hated is not because they killed a lot of people but because they targeted people based on racism and prejudice. Communists killed people they saw as threats (real or perceived) to their ideology and power, and not because of their race, religion or because they were disabled. Again, this makes a difference. Historically we don't have much of a problem with the state killing enemies of the state (how many people shed a tear when Osama Bin-Laden was executed by the Navy Seals?). Obviously the scale on which the communists executed people was far greater, and there's no way that those millions killed by Stalin were all legitimate enemies of the state but there is an emotional difference that exists here.
It should also be pointed out that comparing Nazi Germany to communism in general isn't really a genuine comparison. Communism in Stalinist Russia was very different from the later years of the Soviet Union after Khrushchev's de-Stalinisation. It was still a brutal, repressive, and totalitarian regime, but nothing like it was under Stalin, or what Germany was under Hitler. A more fair comparison would be communism to fascism in general, and so including Mussolini's Italy and Franco's Spain. Both of these regimes are considered bad in comparison to capitalist democracies by most, but neither is seen as the same sort of evil as Nazi Germany. That's because it isn't about being a brutal oppressive regime or how many people you have killed (do you count the 465,000–2,500,000 civilian dead during the Vietnam War against the USA?). No, the reason the Nazi's have a special dark place in history is because they engaged in genocide and because they invented a whole, gruesome, machinery of death to accomplish that goal.