Uuuugh, one of my pet peeves. The word 'theory' has several meanings. In science, it does not mean 'guess' or as the article puts it, 'speculation'.
A scientific theory is an explanation of some aspect of the natural world that can, in accordance with the scientific method, be repeatedly tested, using a predefined protocol of observations and experiments.
Gravity, for example, is a theory. That doesn't mean we guess there is gravity, it means it is something that can be tested and measured using the scientific method.