"¿Hiciste mucho dinero con tu restaurante?"
Translation:Did you make a lot of money with your restaurant?
Both seem fine to me, as a native speaker of Am English.
To me, "from your restaurant" sounds a touch extractive or exploitive - as if the subtle implication might be that the person was in it mostly or only for the money, and didn't care about the restaurant. The preposition "from" suggests separation. Meanwhile, to me, "with your restaurant" sounds more like the person was in it fully, and not simply to make money. The "with" suggests unification rather than separation. This effect is admittedly subtle, but it is there - at least for me.
Sometimes DuoLingo lets you get away with this and sometimes not. In Spanish the difference between a statement and a question is largely just inflection, but in English we (normally) change word order and use an auxillary ("do/did"). It's good practice to get into the habit of reordering the words to make questions more like their common English form.
Do you mean "have you made..."? That would be the present perfect tense, has hecho, the Spanish version here is the preterite tense.
The nuanced differences in meaning aside, Duo's trying to teach these different tenses and grammatically equivalent translations. Mixing and matching might be fine on the job, if the other person gets what you mean, but here you're being tested on accuracy and developing your chops. Relaxing the rules comes later!