My gut feeling tells me the floor under my feet is solid, but it isn't really. My gut feeling is that time and space are absolutes, but now we know they aren't really.
The big advances in scientific understanding have all confounded our intuitions, all of which evolved not because they were true, but because they were useful.
The "trained and organized common sense" view of science as advanced by T. H. Huxley was given a thorough kicking by, amongst others, Lewis Wolpert in
The Unnatural Nature of Science, where he argued (unarguably, in my view) that the more sophisticated that science has become and the more we've discovered about the world, the less reliable our common sense realist intuitions about the world become. To stand on the floor or sit on a chair, and to be able to know that we're not quite actually in direct contact with either - that's true, but unnatural.