Here's why:
* "Command" in this context refers to mastery or control. We use "command *of*" something, not "command *in*" something.
Correct ways to say it:
* She has a good command of English.
* She has a good command in the English language.
* She is proficient in English.
* She speaks English well.
The correct preposition "of" indicates possession or control over the language.