Scientific theories are much different than layman's theories.
I think you're confusing theory with hypothesis. I'm not a scientist, but I know that when scientists use the word "theory," it means that tests and analyses have consistently confirmed the hypothesis.
Which is why "M-Theory" is such science fiction bullshit. You can't test for it. It's not falsifiable making it hack science. To a person who studies science, bringing up m-theory is no different than a creationist claiming "God did it!"
The question of whether a hypothesis is a theory depends upon how many tests or evidence you think is necessary for it to become a theory. M-theory, for example, is based upon string theory, which can be tested via microgravity experiments and particle colliders. Most scientists who study string theory seem to agree that there are at least 11 dimensions/branes/planes/whatever you want to call them, as that's the only way that they can get the math to match existing theories.
Now, the "theory" that these branes collided in order to make "bubbles" that create multiple (maybe infinite) universes is definitely more of a hypothesis, as we don't really see any evidence of that and don't have a way to test it, nor do we have an existing mathematical framework to try to fit that hypothesis into.
At any rate, you get to a point where any theory has an assumption. If it didn't, it wouldn't be a theory. Some "theories" may have more evidence than some "hypotheses," but they all have to make a conclusion based on an assumption. And that assumption could be wrong.
Until we find something definitive that clears up assumptions on either side, there won't be a prevailing belief that is verified as true. The Higgs boson does not, at this point in time, appear to be that definitive discovery that we need to rid ourselves of assumptions and identify a clear, completely factually based conclusion. It gets us further along in our understanding, but I think that it will create more questions than answers.
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