The DC Metro is a horror. God, where to begin (and sorry in advance for venting - but I lived in DC for 4.5 years, in which I took Metro multiple times each day, and the experience still haunts me...)
First of all, the system is extremely unsafe. The 2009 accident on the Red Line (mentioned above - killed 9 people) is only the tip of the iceberg. It became public knowledge then that the automatic train signalling system - the one that's supposed to slow trains so they don't crash into each other - was completely broken, so that trains on the tracks would not appear in the system. This major problem was well known inside Metro, but they just didn't do anything about it. Before and since that accident, there's been a history of near-misses and other accidents that so far have only killed Metro workers on the tracks. The root problems remain unresolved, though, and Metro's overseers have no incentive to do so because oversight is divided up among several jurisdictions. The system should arguably be shut down totally for safety reasons, but the Feds won't allow that because their employees couldn't get to work. Unionized employees are also protected and almost impossible to fire - even if they're running prostitution rings from Metro stations! (This actually happened - Google it).
The bus system is also hugely unsafe, but that's because the drivers in the region are breathtakingly reckless, and bus drivers often have serious criminal records. This is a problem regionwide - I've seen Maryland's Ride On bus drivers refuse to stop for pedestrians in crosswalks and actually nudge them out of the way with their bus - but Metro is the worst of the bunch. For entertainment/horror value, check out the reports of the Metro driver that literally jumped out of his bus during the route to punch a guy dressed as McGruff the Crime Dog, who was doing a crime-prevention thing in Columbia Heights. If I recall correctly, the union got the guy his job back...
As mentioned before, routine (non-critical) infrastructure maintenance is appalling, particularly on escalators. I'm convinced there's huge illicit activity going on with Metro contracting. Escalators are out of service for months, sometimes they suddenly start/stop/reverse with passengers walking on them, no one can fix anything properly. This is a critical problem given that some of Metro's busiest stations are located far deep underground, so older people or those with a disability can't easily hike up a turned-off escalator.
On a more business strategy note, the system is a hybrid city subway/regional commuter rail one, which means it's not terribly convenient for city residents. It runs too infrequently during non-peak times to be a convenient way of getting around the city, and while it's trying to become more like a big-city subway, it skips a lot of major areas (H Street NE corridor and Georgetown, most notably). They've tried to make it more useful to city residents, which is appreciated, but the early closing hours are problematic, and they keep threatening to end those due to funding problems. At any rate, trains now might run only every 20 minutes during non-rush times - that's absurd for such a large city as DC.
Much of the problem is that oversight and funding are split three ways - DC, MD, VA - and Virginia Republicans, as always, balk at spending money on public services. Regional corruption and race politics also play a huge role in ensuring dysfunctional management that fails to respond to the system's serious needs - the Metro union as well as many politicians view the system as a patronage slush fund for the black community, and any efforts at reform get turned into a hugely vindictive fight for political control. The union head has in the past accused people trying to improve Metro oversight of supporting the return of slavery. Small wonder most regional authorities just steer clear of Metro dysfunction entirely, as long as there's no major disaster to respond to.
On a daily commute level, the constant delays, construction, and reduced train load mean that it my commute from downtown Silver Spring into downtown DC went from about 25 minutes to 45 after the 2009 accident; an hour isn't terribly uncommon. Also, even at a station close to the start of the Red Line, it became very difficult to get a seat during the morning commute. Almost three years later, it's still not even close to normal. The Red Line is by far the worst of the lines, in my opinion, but the problems are prevalent all throughout the system.
I moved back to NYC last year, and I feel so much calmer now that I don't have to take the DC Metro anymore. Yes, DC's trains look clean and have comfy padded seats, but the system is a nightmare if you have to deal with it every day. I think lots of DC residents overlook the city's many immense flaws either because they've never lived in a world-class city (hey, DC attracts lots of "Middle Americans" who don't much like the rest of the world, let alone NYC) or because they've just grown used to making excuses. But I'll gladly take NYC's subway at 2am on a Saturday during construction over the DC Metro at 8:30pm on a Thursday. At least in NY I know roughly when I'll make it home.