I admit to being initially against the Main Street rail line, on strictly transport-efficiency and cost grounds. I was ultimately won over by the sheer cool-factor and convenience, plus some arguments by Charles that the line could act as a terminus for the heavy-rail commuter lines I really want to see built.
So it's with no small sense of deja-vu that I find myself reacting negatively to the possibility of a subway line in Houston (ie, build the expansion of the light rail underground to reduce the collision-with-ignoramuses problem).
The main problem is not flooding - Boston has an extensive subway system too, and the Atlantic hurricane season is just as vigorous as the Gulf. Not to mention the fact that Intercontinental airport already has a mini-subway which was expanded for the new terminal, and that there are plenty of below-grade roads in town. A big storm like TS Allison will flood things no matter what, and even Boston had to send divers into Copley Square station on occasion.
Nor is construction as severe a problem as you might imagine. It is easier to simply open th eground, dig down, and lay track than it is to tunnel - and by closing up the line as you progress, you could mitigate the blockage of local businesses problem.
The real problem is cost of operation. If I recall correctly, there isn't a single subway system in the United States that pays for itself - even new York and Boston have to partly subsidize their lines (I am open to being fact-checked on this score). The cost of running a useful line will be quite high and ridership on the above-ground light rail line has not been conducive to rosy estimates of future traffic. I have to question whether any additional light rail lines can be built within budget for a city that is already facing severe challenges to paying its pension plans and whatnot.
The population density of Houston is just too low to support a subway system, IMHO. A commuter rail line, however...