You get science/gold/culture that is better than what you would get from nothing. The cost is happiness, but annexing and razing cost more happiness, especially in the short term.
but its far worse than that of an annexed city or a newly built city
almost all the puppet's benefits are short term
lets make totals..
unhappiness: less unhappiness short term (several turns, while excess population is genocided or courthouse is being built), but long term -
more unhappiness, as a) courthouse removes 3 per-city unhappiness b) in an occupied city you can control population and build order, to restrict growth or prioritize happiness buildings
gold: more gold short term (as theres no courthouse) but less gold long term, as a) puppets build everything so their maintenance rises b) it takes them ages to build banks and stock exchanges as they would always work plantation tiles instead of mined hills.
science:
much less 'thanks' to the additional 20% penalty and inability to run scientists and build science buildings in time.
faith: you cant add faith-purchased buildings there, period.
culture: puppets dont increase policy costs and thats great. although, you cant buy religious buildings there, cant prioritize amphitheaters etc, and theres a -20% culture penalty on top of that, so even in this aspect puppets can be worse (unless you have got a dozen).
NWs: the only thing puppets are undoubtly good for.