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The denominations that dedicate their churches in this fashion tend to be those with a more centralized structure. As far as I know the decisions are usually made by consultation between the local congregation and the church authorities. I've been part of one Anglican church where the choice of a name was clearly that of the congregation, with the approval of the central authorities.
Other organizations can also have an input. I was part of one congregation where the choice of name was vetoed (or at least recommended against) by the Fire Department, on the grounds that there was already a church with that name in the town, and the fire trucks might be dispatched to the wrong one. In this specific case "Saint Luke" was the preferred name, since the church was to share a building with a medical centre (St. Luke was a doctor). However in the end "Saint Francis" was chosen.