The major reason is because of the Nazi party's ideology. Now, technically both countries had a non-aggression pact until 1941. But, both sides knew that wasn't going to last. From the perspective of Nazi Germany, co-existence with USSR was simply not an option if they were to continue to practice the idea of Aryan races' supremacy over others. Hitler and other Nazi party members denounced communists and slavic people before, and as USSR is the country that represented both parties, Hitler simply believed it was necessary for him to take over USSR. Thus, alliance with them was not an option ever for Nazi Germany.