The concepts never made sense, they simply had far less good alternatives in the past.
If the answer is no, this should give you pause. A thought experiment. Consider the alternatives:
(a) that we finally removed all irrationality from our understanding of reality, and you happen to be living in this golden age, while the centuries and millennia extending before you were dominated by irrationality;
(b) that it is very hard to spot irrational beliefs when you are immersed in the culture that produces them.
Which one do you figure is more probable?
Sorting beliefs into "rational" and "irrational" is a bit too black and white imo. We have (scientific) models. We can support (but not prove), question or disprove them by applying the scientific method. There are beliefs/theories/models of varying popularity in our current scientific knowledge that are wrong but that we haven't disproven yet.
You might differentiate between "we're looking for ways to disprove them" (i.e. being scientific) versus "we apply confirmation bias" (i.e. being superstitious) to distinguish rational and irrational beliefs. But my point is that there is a third option that is missing in your list:
(c) we are suspicious of them (because they don't make sense?) but haven't yet come up with a way to put them to the test.
IMO it's mostly (c) but with a hearty helping of (b) on the side.