The first thing to clear away is the assumption that this belongs to Rome. Many Protestants carry a mental map on which Christianity divides into two territories, Catholic and Protestant, with everything ceremonial assigned to the first and the Orthodox appearing as an eastern annex to Rome that kept the ceremonies and lost the Pope. Consider, then, who actually makes this sign. Roman Catholics do, and Eastern Orthodox do. So do the Copts, the Syriac Orthodox, the Armenians and the Ethiopians, whose churches broke communion with both Rome and Constantinople after the Council of Chalcedon in 451, and so does the Assyrian Church of the East, out of communion with everyone since the Council of Ephesus in 431. These are not churches that borrow from one another; they have spent most of Christian history anathematizing one another over the person of Christ. A practice common to all of them is not a Roman peculiarity. It is an inheritance older than the divisions, which is to say older than 431.
Then there is the awkward matter of the Reformers. Luther's Small Catechism of 1529, written to be taught in ordinary German homes, gives a morning and an evening prayer, and both begin with an instruction about the body before any words at all: “In the morning, when you get up, make the sign of the holy cross and say: In the name of the Father and of the Son and of the Holy Spirit. Amen.” Luther demolished a great deal of medieval practice; this he kept and taught to children. The 1549 Book of Common Prayer retained the signing of the child's forehead at baptism and retains it still, and when the Puritans petitioned James I in 1603 to have it removed, the English Church defended it in Canon 30 of the Canons of 1604 by direct appeal to the usage of the primitive Church. The rejection came from the Reformed stream, and their concern was not imaginary, since late medieval popular religion had accumulated much that functioned as folk magic.
Notice what a Protestant is being asked to believe if the sign of the cross is a corruption. He has to believe it is a corruption that Luther kept and taught to children, that the English Reformers defended in canon law by appeal to antiquity, and that four separate families of ancient churches, which excommunicated one another over Christology, all preserved independently for fifteen hundred years.