But some theories are so well supported that they are "practically" certain. Of course it is right that in science no one is 100% certain of their conclusions. But, for example, the confidence we can have in some well supported theories is very high, asymptotically approaching 100%, and is established to such a degree that no one spends any research time trying to find an alternate explanation (just as there is no serious research into Flat Earth, or Phlogiston, Geo-centrism, or Astrology). But, philosophically, the level of confidence cannot be 100%. To put any weight on the lack of certainty for quantum theory, evolutionary theory, atomic theory, or the helio-centric model of the solar system would be perverse, arbitrarily contrary, and unproductive. These are among our best theories, and until something better comes along, they are best treated as being essentially correct.
I am confident (though not certain) that 100 or 1000 years from now there will be some entity that occupies the logical "slot" that we currently call an atom, and that two oxygen atoms and one hydrogen atom will continue to be the basis of a wet substance called water. The model of the atom has changed, and will probably continue to change over time (for example, the models proposed by Democritus, Dalton, Thompson, Rutherford, Heisenberg/Chadwick/Bohr, up to the current quantum mechanical "cloud" model). Atomic theory may be subsumed (and probably already has been) as a special case of some more comprehensive theories of matter and substance. But it will still have applicability in chemistry and normal daily living, just as Newtonian physics, though extended by Relativistic physics, is still appropriate in a subset of cases. F=MA is probably (though not certainly) going anywhere. As Stephen Jay Gould wrote,
In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms.
On the other hand, we do have 100% certainty in areas involving "analytic statements" (Kant), sometimes called "relations of ideas" (Hume), where a statement is true or false based on its meaning or definition (for example - no bachelors are married, 2+2=4, triangles have 3 sides). When the premises are true, and valid logic is used, then the conclusion is fully contained in the premises and 100% certainty is established.