"Tomato is not a vegetable."
Translation:टमाटर सब्ज़ी नहीं होता है।
होता है makes it a general statement of fact. The sentence you suggested would also translate to the same thing but it wouldn't mean the same and it would feel unnatural.
Better English would be: Tomatoes are not vegetables./ A tomato is not a vegetable.
I agree. I'd prefer
A tomato is not a vegetable.
because it is closer to the Hindi sentence (singular) and in line with other sentences in this course that make general statements.