I like the argument for 'benefit of the doubt' where the question of whether we exist/actually have free minds is concerned. Basically, it is entirely possible that we're just brains in jars/imaginary/whatever. But it is least beneficial for us to operate based on that theory. We operate on the best assumptions we can make, because in the event that they are true, we are then taking the most beneficial form of action. So we build up the basic things we can know, as Descartes did - I am aware that I think, therefore I most likely exist in some capacity, and so on. None of this can be taken as fact, though.
We can only really determine fact based upon assumptions like the ones made above. All fact comes with the unspoken qualifier of 'assuming that I exist, and that my senses do not deceive me, then the following is true/false'.
I am doing a project on the philosophy of science at the moment... we are asking this a lot!
I think I tend to agree with you, I think of facts/knowledge and scientific laws as things we cannot ever objectively say, this is 100% definitely true. Not just because we might all be Putnam's brain-in-a-vat... but because history shows us this. It shows us that things we thought were empirically 100% true turned out to be approximations, and that things we perceive are sometimes false.
But it's a useless way to look at the world, so giving your senses and logic the benefit of the doubt, or looking at things as what is most probable, this probably is true, this probably isn't true, etc, allows us to make sense of things, talk and discuss and do science meaningfully, etc. We can say, this theory is our best guess at the moment, this theory is probably true... these days most scientists don't see science as "facts that are true" but in a more probabilistic way... accepting that they might be wrong, and if they are, well that's science for you!
In response to beancounters points on faith... I think actually the fact that science admits things can be wrong, this might not be right, is what distinguishes it from faith. Faith is about saying, I 100% trust in this, and if there is evidence to the contrary that evidence is false, because I have a commitment to my faith that overrides it. Whereas science is about saying, if the evidence says otherwise, I'll believe in it, I may be wrong.
Ah I just wrote an essay on this... why am I essentially doing more work, for fun?