First of all thanks to this wonderful forum for all the great suggestions. We will be arriving in florence novella station from train from venice. We would like to rent a car and head to chianti area to our agritourismo (found a great one thru this site). People are telling me its a nightmare to drive from borgo ognisaanti because of ZLT and other complicated traffic patterns.Someone told me they got clear directions and still got a ticket while coming back to return the car. Is it worth taking a cab or train to the airport and renting from there or is there any other small town rentals before novella where we can get off and rent a car?

Bologna is the last stop I think on fast trains between Venice and Florence so no option to get off at smaller town. there are Florence rentals outside the no-go zone I believe -but you have to go to SMN - I'd rent in Florence and work out details - I assume major car rentals are outside the no go zone or have some way to get you out.

Why not rent car in Venice and just head to Chianti without hassling with Florence?

I was going to post just what Pal suggested. Rent at Piazzale Roma in Venice drive straight to your agriturismo.