That's one of the many things that's difficult to understand about the Holocaust. Obviously, the mass transportation of Jews ranked very high on Hitler's list of priorities. His faulty military strategies, such as invading the Soviet Union, show lack of determination and realism to win the war. Apparently, his dream of building an Aryan nation was just as important to him.
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Perhaps transporting them by rail kept them from the sight of normal German citizens who might otherwise have been appalled and refused to go along with Hitler's policies.
Another question to ask is why Hitler didn't just kill all the Jews and other non-desireables as he (actually his minions) did by burning villages, shooting masses of people, and starving whole ghettos.
You ask an interesting and important question.
Most of the death camps both in the number of camps and in the number of victims were not located in Germany. They were located in other countries such as Poland. Many more Jews were killed in Poland than in other countries including Germany.
There is a controversy even today about how widespread the knowledge of the death camps was for the non Jewish population. Many claimed that they did not know, others say that they had to know what was going on.
Some believe that most Jews did not know that they were being sent to extermination camps. The argument goes that had they known they would have resisted as they did in the Warsaw Ghetto uprising where surprising to the Germans the population resisted and fought back and was overwhelmed by the German army with vastly superior numbers, ammunition and supplies.
One of the most sobering experiences in my life was several years when I visited Auschwitz in Southern Poland which was the largest and most notorious German prisoner camp. Many put the number of victims at Auschwitz as between 1,100,000 to 1,500,000 with more than 90% being Jews. The figure for the number of Jews killed is about 6,000,000.