I'll start by stating up front that the lack of good condom research is a thorn in every sex educator's side. In vitro research says they work, and retrospective studies say they work, but there haven't been nearly enough of the randomized, prospective trials that are the gold standard of research. Thus, in 2001, we got stuck with an HHS report which said that there wasn't enough evidence to say that condoms were effective at preventing anything except HIV and gonorrhea - and gave the anti-sex lobby something to point to as saying that condoms don't work. (That isn't what the report said. All it said is that we don't have enough evidence to conclusively prove that they do. That's a very different thing. For the conditions where there was evidence, condoms looked good. They still do. Furthermore, for the reasons described below, condoms probably actually work better than we think they do from studies.)
So why is it so hard to do research on condoms? In large part, it's because people are aggravatingly fallible - both about using condoms and about keeping records. It's extremely difficult to get an accurate picture of when people have sex and whether they use a condom each time. Not only is recall of these things difficult, but there is a known problem where study participants tell researchers what they think we want to hear. In studies of condoms that means they mostly say they used condoms more consistently then they did, which can make condoms look less effective than they are.
Another thing that makes condoms seem less effective is that it's difficult to pinpoint exactly when any given infection occurred - since new STDs are often silent for months or even years at a time. Therefore, unless you test people more regularly than is practical, it's impossible to tell if a disease was transmitted before a condom lapse or afterwards. The only time it isn't a problem is if you know you have a group of completely consistent condom users to compare to your non-users... and that's a pipe dream.
So, to address the question that my readers probably care about the most..... Are condoms effective? The article makes a very good case for why the answer is yes. It certainly said nothing that would dissuade me from my belief that they're our last, best hope against STDs.