Hey Mehrdad,
'Are you IN home' is definitely incorrect.
'Are you at home' is completely fine.
However, I would say that we'd simply say 'Are you home?'
With regards to the ESL point, yes, my first day at school is better.
'In school' has a slightly different connotation.
'Michael's still in school'. i.e. he is still a student and therefore studying at school.
Hope this helps!
Matt