Keeping ~10^6th protons contained for minutes is a long way from 10^28th protons contained for years. Anyway even with antimatter you are still bound by the E=V^2 problem so launching a large ship at 1g for 2 months might be possible with anti matter but the energy requirements become insane. For that matter generating atimatter is ridiculously inefficient, if you had perfect containment and converted the all the world electricity production into antimatter using current methods you would not be able to launch a bottle rocket let alone a useful ship.
