In the broadest sense, the most important long term cause of the Amritsar massacre of 1919 was British colonial rule of India. The massacre, at its heart, came about because of Indian anger at being ruled by Britain and by British determination to hold on to their empire by whatever means were necessary.
Since the mutiny of 1857, distrust had grown between the Indians and the English. This distrust was exacerbated by World War I. During WWI, India was vital to the British war effort. Over a million Indian men served in various capacities outside of India during the war. Indian leaders (in addition to the British rulers) sent material aid to the English as well. However, the Indians were not treated well or (to their minds) sufficiently appreciated for their help. From the British perspective, the aid in the war seemed less important than the fact that Indians in 1919 seemed rebellious. The aid in the war also seemed less important to the British than the fact that there had been things like the Ghadar Conspiracy. Indians, then, felt underappreciated and the British felt the Indians were treacherous.
The long term causes of the massacre, then, had to do with the rising animosity between British and Indians that can be traced at least back to 1857 and which was made much worse by the events surrounding WWI.