Yeah, it doesn't make much since if you think in terms of how many transistors are needed to implement each of them as the microcontroller probably uses hundreds of thousands more transistors than a 555.

That said, given reasonably recent processes die size for both are probably pretty close (I reckon most of the size of a modern 555 die would be the points to place the wires to the package) and with pretty similar yields (pretty close to 100%)

I wouldn't be surprised if the reason has something to do with economies of scale since a cheap microcontroller can pretty much be used for the same things as a 555 and a whole lot more than that, so it makes sense more of the former are manufactured than of the latter, plus I bet the process generation used in making the microcontroller is probably more recent and hence one where there are more fabs operating. This latter reason would also explain why this more recent 32-bit microcontroller is actually cheaper than older 8-bit ones with less built-in memory and fewer peripherals (such as the ATTiny ones).