It is a matter of how the language develops. Normally, you would only hear "She is good at cooking." 'In' is technically correct, but you would never hear it. However you WOULD hear "She is good in sports" AND "She is good at sports." There is no logical reason that this is so, it is just how the language developed, as I said.

In British English it would be "at" for all the above examples. Good at cooking, good at maths, good at sports.

1. good at something 2. good in a subject (maths, physics, chemistry, cooking) If the subject at school is "cooking", then you are good in cooking. Otherwise you always use "at".