2nd Avenue subway [0] requires about 8.5 miles worth of tunnels (several hundred feet of which were already dug back in the 70's) and it's budget is $17 billion. Of course that whole cost isn't just for digging tunnels, but it's a clear indication that digging tunnels (especially in dense urban areas) can be extremely expensive.

[0] http://en.wikipedia.org/wiki/Second_Avenue_Subway

There is a very large difference between building complex tunnels and a simple hole in the ground. The cost for drilling a straight exploratory/mining hole was 10 Million/km in the 70's and 80's[0]. I can easily imagine this being cheaper by a factor of 2-5 with current advances. Not to mention this concept has a lot of synergy with mining companies.

[0] http://facstaff.gpc.edu/~pgore/geology/geo101/interior.htm

There is a difference, but it's not necessarily large for deep drilling. Once you start drilling large diameter holes deep into the ground, you have to shore up that hole to prevent it from collapsing in on itself. For wells or expiatory holes, water or slurry is used, but that's not an option in this case, so there will need to be a casing involve. Installing that casing so that the pieces line line up perfectly is a complex endeavor (not impossible, it's been done, just not straight forward as "drill a hole")