But surely we can say that some "theories" are more certain than others.
This doesn't seem to get emphasized enough. I agree that there are large differences in the degree of certainty involved.
For example, we can make a good guess that general relativity is not correct since problems arise on the scale that quantum mechanics comes into play. (It may be QM that is flawed of course). However, GR is more "correct" than Newtonian mechanics. And, for the scales where we use it GR tests out as being extremely correct. That is, it is useful.
By contrast the theory of evolution has no well founded hint that it is wrong. It seems to stand up very well against many different tests. It has proven, in addition, to be very useful in many circumstances. On the other hand, there are ways in which it is not "useful". Because what actually unfolds in the very messy, complex real world is enormously contingent the theory can not usually be used to predict [i]exactly[i] what will occur. GR can predict with enormous precision what will occur to, for example, the GPS satillites.
With this in mind we still find Newtonian mechanics "useful". But we know that it is "wrong". What we consider to be 'correct', 'proven' and 'certain' may depend very much on the specific context of the discussion.
Another example is string theory. It is very, very uncertain. No one would argue that it is equivalent to atomic theory. Today we treat atomic 'theory' not as a very certain but tentative theory but rather as a "fact". Note I said "treat". We understand the possibility of finding new information that may overturn the idea but we
act as if it is an unshakable
fact.
My point (lost in words) is that there is, for practical purposes, a continuum from hypothosis to fact. The lines between them are not as sharp and clear as we generally believe when speaking day to day.