Well first off, Stalin forbid East Germany/Berlin access to Marshall Aid. Also, many people in the East suffered from poor housing, food shortages, low wages, and having a lot of their industrial output going to the soviet union. Most east Germans foresaw that no help would be coming to them as the 60's drew near so they just upped and left, because they were free to travel to West Berlin anytime they wanted up until the wall was built. From 1945-1961 about 3 million people passed to West Berlin, sometimes up to 4,000 a day, to find new life in the West. Also, many East Berliners had family and friends living in West Germany/Berlin, making it even more hard on them to live in the East.

Sources: UK History Learning site's section on the Berlin wall