You're confused because those are indeed two completely different verbs.
would mean that tomatoes are standing (perhaps boxes of tomatoes are standing in the corner of a grocery store).
Cколько сто́ят помидоры?
means "how much do the tomatoes cost?".
In the first instance, the verb is "стоя́ть" (to stand); in the second — the one you're asking about — the verb is "сто́ить" (to cost, to be worth).
Не стои́т" means doesn't stand, and often by default it refers to erectile dysfunction.
Не сто́ит" means "[it's] not worth it", "don't do it", "no, thanks" ("not worth it" being the literal translation).
Он/она того не сто́ит" means he/she isn't worth it.
Он/она уже на ногах не стои́т" means he/she is so drunk, that he/she can't even stand upright.
Since in Russian, stress marks aren't used except for learning materials, the only way to know whether 'to stand' or 'to cost/be worth' is being used is from the context. "
Сколько стоит... ?" is pretty straight forward as it's clearly a question regarding the price of something ("How much is... ?"). However, a question starting with "сколько" and followed with "стоит" can in some instances refer to standing. For example "
Да сколько вы там уже стоите?!" means "Just how long have you been stuck there for?!", so the "и" would be stressed in that case.