I encountered this sentence.
「ろうそくが置かれている」
I can tell from context it means something like "Candles are placed", but I'm confused about the usage of ている with a transitive verb. Genki tells me that ている goes with intransitive verbs, yet 置かれる is the passive form of 置く which is transitive. What am I missing?
「ろうそくが[置]{お}かれている。」
does not really mean "Candles are placed." as you stated. That would be 「ろうそくが置かれる。」.
「ろうそくが置かれている。」 can mean two different but related things.
Passive Voice + Present Progress: "Candles are being placed." ← Someone is in the middle of placing candles.
Passive Voice + State: "Candles have been placed." ← Candles were placed some time ago and they are still there.
Which one it means would depend solely on the context it appears in as Japanese is an incredibly contextual language.
"Genki tells me that ている goes with intransitive verbs."
I am afraid to say that that is false. The transtivity of the verb does not matter.
