The main reason why protestant theologians opposed prayers for the dead was because of purgatory. Since they no longer believed in purgatory, they did not need to pray that people would be released from it. Secondarily, praying for those who had died might seem to undermine the doctrine of assurance. But, there are many other reasons for praying in addition to anxiety about someones particular state. True prayer is an out flow of love; if I love someone I want to pray for them, not necessarily because they are in difficulty, but simply because holding them up in God's presence is the natural thing to do. Love does not stop at death, in fact, death could be defined as the form that love love takes when the object of love has been removed. (For All the Saints, N. T. Wright, 2003)
The protestant reformation was a battle for the soul of Christianity, and the gospel in the western church. As with most battles, there are always some who are killed from friendly fire. Fire fights are so intense, that clarity is not always available when needed, and consequently, it is common to hurt and destroy the things we love. Prayers for and with the dead, those who now live in eternity and in the presence of all creation, was one of these casualties from friendly reformation fire. The Catholic Evangelical understands the goodness in praying for and with the dead, while not undermining of the promises and assurances of Christ's salvation for his estranged beloved ones.