Quick answer: Size vs speed vs range.
Long answer:
Engagement envelope: Have you see the size of a SS-N-19 or SS-N-22 vs a Harpoon? Those thing are huge, it's like a small airplane. While it is fast and long range. A high flight profile large size target can be engaged 100+ miles from the ship whereas you'll be lucky to be able to engage a sub-sonic very small target at sea-skimming level at 20 miles out.
Engagement time. A high Mach target that can be engaged 100+ miles give a similar engagement time as a sub-sonic target that can be engaged 20 miles out.
Accuracy: Yea a faster moving target should be harder to hit but it make minimal difference when it's coming straight at you. Arguably, the larger size more than offset the speed penalty.
I think a lot of people is under estimating how hard it is to hit a Harpoon. I think taking a look at how many CIWS systems you see on the last generation of Russian ship gives you an idea how big a threat they felt it is.