They worked on making the car better. If Kimi doesn't like the changes even though the car is faster(as the other driver showed), then boo hoo, cuz that's on Kimi. Ferrari did exactly what they should have done.
People completely overrate how much a car is designed for specific drivers. Teams make cars which they think will go fast. Its then up to the drivers to make the most of it. That's what they are hired to do.
OK, to a quite extent it is probably true. Still, there must be something which suits to one driver better than to another...
Rosberg Sr. was kind of a Mansell-esque driver (you know, one of those "give-me-a-car-and-I-set-the-world-on-fire kinda driver). And in 1986, he came to a team which consisted of the two probably most "clinical" drivers there ever were in F1 (Lauda & Prost). So, they were maybe absolutely contrary to the driving style of Rosberg Sr.
And Rosberg was nowhere in that season in that car. If there was a considerable up-date on the car mid-season which suited to him, he was on pole, immediately (Hockenheim 1986).
Gee, he even looked worse compared to Prost than his successor at McLaren (Johansson) compared to Prost one year later! OK, Rosberg had overall more DNFs in 1986 than Johansson in 1987, but Johansson was even runner-up to Prost in the WDC table after the first three races! And overall, no way is Johansson "better" than Rosberg Sr.
So I think, there must be sometimes indeed situations where the car has been, in a certain way, built around some driver over the years which other drivers with maybe contrary driving styles are in deep trouble with...