Generally speaking, much of theory will have some basis in what we already know to be true, or at least scientifically tested/vetted as true. I will grant you that there are some theoretical physicists out there who've proposed what we would think as rather crazy ideas, however, you have to understand that quantum mechanics allow for some extremely peculiar and to be honest, alien outcomes. We just don't see the world on a quantum level, and it's difficult for us to imagine how things can work the way they do there. For example, getting something from nothing (See: Lawrence Krauss, on youtube) as an explanation of how the big bang is a completely reasonable event in quantum mechanics.
To answer your question though, no, I don't think people go to far in scientific theory. If the theories were accepted blindly, without proper vetting I'd have a problem with it. But, part of being a great scientist is helping to prove others wrong/right, through extensive testing and research. I will say what many people say is either assumed or made up, is simply a lack of understanding in the field.
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