She comes to school by car.

Literal

She [topic-は] car [by-で] school [to-に] comes.

車で (by car) uses the instrumental で for the mode of transport. 来る (to come) implies the speaker is at the school — she travels toward the speaker's location. A simple sentence demonstrating the [transport + で] + [place + に] + motion verb pattern that's fundamental for talking about commuting.