Rutherford's experiments were to test the plum pudding model, namely, the theory that an atom is a sphere is positive charge with negatively charged electrons dotted around the outside. He used Alpha particles because he knew they were positively charged, and so he wanted to test what happened when he bombarded the gold foil with them. He didn't know they were going to get through, that was the whole point of his experiment. Since some of the atoms got through, but only a tiny minority deflected, Rutherford concluded that only a tiny part of an atom is positively charged, with the rest being mostly empty space, and so they threw out the idea of the 'plum pudding' model (in favour of the nuclear model), which would have yielded different results.