'Il pleut' translates to 'It is raining.' If you want to translate word for word, 'Il' = 'It' and 'pleut' = 'is raining.' In French, there's no difference between 'It rains' and 'It is raining' because they're both in the present tense. The 'is' is part of the verb so to speak.
But yes, the reason the translation is 'is it' instead of 'it is' is because it's a question. They're both technically valid, it just depends on your intonation, whether you say 'It's raining.' or 'It's raining?'