"Protestantism" is extremely diverse, and there is pretty much no single way that Protestants do anything. This is especially true of the Eucharist.
Some Protestants do consider do believe that the transformation of the bread and wine into the body and blood of Jesus is real. Others believe in treating the communion elements with special reverence even if the transformation is symbolic or spiritual. The Anglican church, for example, also expects that leftover elements are consumed after the service - usually by the Priest.
For those that don't follow this practice, the elements can be disposed of in any way that is convenient. They can be eaten, thrown out, or kept for next week. A lot pfMany Protestants also don't use actual wine for the communion, but grape juice instead.