The Phlogiston theory was not a scientific theory as it could not explain the facts and evidences. Only after Lavoisier recognised phlogiston as an element that was named Oxygen did phlogiston go the way of the dodo. Science was at its infancy back then and the rules governing how scientific endeavour should function were non existent at that time.
Today science has sets and rules that it abides to in order to function. So the term theory during the days of phlogiston was not the same as it is meant in the scientific world. It was used in the same term as in literature as speculation or something unproven.
Science is an ever evolving thing. It grows as knowledge grows. Just as we humans started of as mere babes hardly able to fend for ourselves and are now adults holding our destiny in our own hands.
You may find the documentary interesting as it shows what life will be like in the near future.