I can't remember where I first read about the cost of Tunnel, but it's stuck with me as a great example of elegant design.
Tunnel has two parts and each one matters in different phases of the game. If you buy Tunnel early, it's almost always because you want to make use of the gold-gaining reaction. The 2VP don't matter at all. $3 for that reaction is reasonable. It doesn't need to be more expensive because there is usually further opportunity cost in picking up a discarder and getting the cards to line up.
But in the late game, the reaction doesn't matter much anymore. There's not enough time for the gold gaining to matter. This is where the 2VP comes into play. In the late game, you'll often be happy to pay $3 for 2VP even if there's no way to make use of the reaction at all.
So yeah, Tunnel can seem like a steal because both of its parts could be worth $3 separately. But since they matter at different points in the game, it works out.