Firstly, they are usually only focusing on direct emissions, which makes the transport sector look less important (therefore people will be less motivated t change).  It also probably favours car travel more than it should, as their are tens of billions of dollars associated with this industry and the impacts it causes (many times more than other modes).  All these industries have associated greenhouse gases which are indirect emissions for car travel.

Second, the calculator takes a snap shot - what the emissions are currently.  It is important to look at potential development, because different modes run on different power (such as petrol cars vs electric trains), and the potential to reduce the emissions associated with these power supplies is very different. 

Thirdly, these calculators need a way of allocating responsibility of emissions for privaely run vehicles, as well as publicly run transport networks.  Private seems easy enough, because the people using it, are responsible for the type of car they have, the fuel they use, the route they take and how many people are in the car.  As for the public transport user, they have no control over these factors.  A snap shot of current conditions (average ridership etc.) is often used, but this is rarely optimal conditions, and public transport is often misleadingly seen as an unattractive way to reduce one's "carbon footprint"

I'm interested to have your view and experience with carbon calculators.  Do you take them as bible, are you skepical, and would it convince you to change your behaviour?