I have User which has-one Person. So User.person is a Person. 
I am trying to get a list of User from a list of Person.
I tried the following:
>>> people = Person.query.filter().limit(3)
<flask_sqlalchemy.BaseQuery object at 0x111c69bd0>
>>> User.query.filter(User.person.in_(people)).all()
NotImplementedError: in_() not yet supported for relationships.  For a simple many-to-one, use in_() against the set of foreign key values.
What is the best way to get a list of Users where User.person is in that list of people? 
As the error message helpfully tells you, you need to use in_ against the foreign keys instead:
User.query.join(User.person).filter(Person.id.in_(p.id for p in people)).all()
Since you're going to query for both anyway, might be better to do a joined load and then get the people using Python:
people = Person.query.join(Person.user).options(db.contains_eager(Person.user)).limit(3).all()
users = [p.user for p in people]
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