Huge transportation projects obviously cost a motherload, but as experience shows, the actual price often ends up being a mothermother load squared. Why does it happen is a good question, but it is definitely a possibility that the initial deadlines and costs outlined in the project bids are set based on what the companies think will land them the job, not what it will actually cost. If you want to see examples of billion dollar projects that ended up costing up to ten times more, check these:
The great project of Boston that rerouted the Central Artery, the chief highway through the heart of the city, into a 5.6 km tunnel. The planning of which started back in 1982 while the actual construction began in 1991. Initially it was expected to take 7 years, but ended up taking 15 years (it was completed in 2006). The cost of the project was promised to be only $2.8 billion, however, by the time it was completed, the cost had risen to almost 15 billion and after fixing all the problems the "completed" tunnel had, the final cost was around 22 billion dollars (which won't be paid until 2038). Well, it went up just slightly, right?
Channel Tunnel or Eurotunnel is one of the most expensive projects in Europe, a 50.5-kilometre rail tunnel (of which 37.5km is under water) connecting United Kingdom and France. The idea of the tunnel was born already back in 1802 from the womb of Albert Mathieu, a French mining engineer. Obviously, back then it was just an idea, but more than 175 years later, in 1988 the construction started and it was completed in 1994. The initial cost of the project was estimated at 2.6 billion pounds. Compared to Big Dig the final cost was quite close to it, at 4.6 billion pounds. But then again, it's 80% over budget.
The construction of Dubai Metro started in 2005 and the cost of the project was estimated to be $4.2 billion. It ended up costing nearly twice as much, $7.9 billion and out of the initially planned 5 metro lines only two have been completed.
New San Francisco-Oakland Bay Bridge
In 1996 the 10-lane 7.18 km long bridge was estimated to cost $1 billion and take seven years to complete. By the time it was completed, it had taken ten years and $6.5 billion.
I'm not sure if we should be surprised of such changes in deadlines and costs, especially considering the massiveness of the huge transportation projects and the millions of variables that can influence the planning and construction process, but it sure shows that none of them should be taken seriously.