A fact in science is an objective, verifiable observation. It differs from a theory, not in that a fact is true and a theory isn't, but in that theories explain or interpret facts.
Science relies heavily on observed phenomena and the empirical method. It could be philosophically argued that no aspect of our reality can be conclusively proven to be true, even that which we can directly observe. The logical conclusion of this argument is that no scientific fact can be shown to be absolutely, concretely true, especially facts that have not been directly observed. However, we can have so much evidence in favor of something, and we can be so sure of something that there is no viable reason to doubt it, and thus it would be plain stupid to doubt it. This is what a scientific fact is: While in common parlance it is something that is absolutely true, in science it might as well be absolutely true.
The fact that science relies on directly observed phenomena does not hinder the ability of a scientist to come to a logical conclusion given the evidence concerning a phenomenon that hasn't been directly observed; in fact, he is using the evidence from direct observations to reach this logical conclusion.
An example: It has been observed, ever since the first moments humankind has been around to take note, that things fall down. This observation has been consistent since we've been around to observe it. However, we have not directly observed whether or not things will continue to fall down tomorrow, and they very well might not. But we have consistently observed that things fall down day after day, year after year. We have very little reason to doubt that the phenomenon will ever change. We have so little reason, in fact, that anyone who does doubt it given our current evidence would be viewed as purely and patently insane, even though, strictly speaking, the possibility cannot be totally excluded.
Quite a few scientific facts are commonly portrayed as inconclusive and uncertain by critics. A famous example is the phenomenon of evolution. These critics fail to realize that evolution and other scientific facts are called facts for a very good reason: There are mountains of concrete evidence in favor of these and other scientific facts, and virtually no appreciable evidence against them; thus, there is no viable reason to doubt these facts given our current evidence, and indeed it would be patently stupid to do so.