Theory, n. a well-substantiated explanation of some aspect of the natural world that is acquired through the scientific method and repeatedly tested and confirmed through observation and experimentation.

I think you are referring to philosophical theories. In science a theory can be a "fact". Ex: Theory of general and theory of special relativity, Theory of evolution by natural selection, Quantum theory, etc.

Theoretically (excuse the pun) they could all be disproved some day but most people know they will not be.

To cite wikipedia for lack of a better source:

"Scientific theories are the most reliable, rigorous, and comprehensive form of scientific knowledge, in contrast to more common uses of the word "theory" that imply that something is unproven or speculative (which is better characterized by the word 'hypothesis'"

[0] http://en.wikipedia.org/wiki/Theory