It's not that I think this security theater is so logical or effective. I think it's often a waste of money and resent the ubiquitous impositions it creates, although I think this may change somewhat after next year.*
But it does attempt to address some basic realities: the most attractive place to cause damage is at the incoming station, where a crowd will be waiting for the train; getting a parcel onto the train will require passing armed police/troops (and who knows what else? dogs? electronic detectors? the uncertainty is meant to erode a terrorist's confidence); there's a reasonable chance a bomb would be carried by a human, given a) the demonstrated preference for suicide bombings among Islamic fundamentalists and b) the relatively low participation by Islamic countries in winter sports, reducing the probability of a would-be martyr inadvertently blowing up co-religionists.
In a nutshell, the sight of heavily armed guards is, sadly, meant to look familiar and imposing to potential terrorists - because many Middle Eastern countries have paramilitary-type law enforcement. Polite and discreet security (eg the US secret service guys in their suits, or friendly-looking beat cops) wouldn't make a terrorist feel especially nervous - the same way that kids don't take mall cops very seriously because they don't have guns or tasers.
* When I go downtown, the subway station restrooms are still locked with increasingly faded stickers on them saying 'closed for security reasons due to September 11 attack'. The 10 year anniversary of that event will be a sad one, but at the same time a decade seems to be the difference between past and present for most people. So my hunch is that after it passes, there will be a lot of questioning along the lines of '10 years on, do we still need this?'
In that light, and with an election the following year, the question of budgets will also arise. the Department of Homeland Security costs about $56 billion/year. For comparison, the Department of Justice (including the FBI, DEA, and all the other law enforcement agencies) costs less than half that amount. The entire Federal court system costs under $7 billion/year. So I think a reassessment of our security strategy is on the horizon.