Scientists change a model when new evidence does not fit it. The model of the atom has changed several times.
Before the electron was found, atoms were thought to be tiny solid spheres. Then J. J. Thomson discovered the electron and proposed the plum pudding model: the atom is a ball of positive charge with negative electrons embedded in it, like plums in a pudding.
In the alpha particle scattering experiment, Rutherford's team fired alpha particles at a very thin sheet of gold foil. Most alpha particles went straight through. A few were deflected by small angles, and a very small number bounced almost straight back. The plum pudding model could not explain this. Rutherford concluded that the atom is mostly empty space, and that its positive charge and most of its mass are concentrated in a tiny central nucleus. Alpha particles are positive, so they are repelled by the positive nucleus.
Later, Niels Bohr explained that electrons orbit the nucleus at set distances, in fixed energy levels or shells. This is the Bohr model, and it is the model of the atom you use at GCSE.
