Before the Cold War many argue the US and the Soviet Union were natural enemies over ideology but one might argue then we should have had and still have a cold war with China. Why do you think we did with the Soviet Union and did not really with China?

The United States did not trust the Soviet Union ever since Russia backed out of WWI despite receiving American aid to stay in the war.  During the 1920s American leaders were on high alert to prevent a Bolshevist takeover or an anarchist uprising and many people of Russian descent or sympathies were deported.  It was not until the Franklin Roosevelt administration that America finally recognized the Soviet government that had been in place for over a decade.  After WWII the United States criticized the totalitarian  puppet states which sprang up in Eastern Europe in the wake of the advancing Soviet armies.  The United States thought that all Communist regimes were taking orders from Moscow and that the next world war would take place between the U.S. and the Soviet Union.  It did not help when the Soviets clandestinely exploded an atomic bomb.  
America initially did not trust the new Communist regime in China that ousted its WWII ally Chiang Kai Shek.  China fell to Communist forces during the Truman administration, and it was not until the Nixon administration that American-Chinese relations normalized.  Nixon saw an opportunity to drive a wedge between China and the Soviets and he took advantage of this.  Nixon turned a blind eye to China's human rights' abuses and even built trade relationships with the nation that still exist today.  America needs Chinese trade more than that of the former Soviet Union, and that partially explains why the U.S. has better relations with China than with the Soviet Union.