We can all sit here and reel off bad experiences. However, each post just seems to give one bad experience that doesn't demonstrate and indemic problem.
I have no affiliation to business travel agents, I once worked in a leisure agent part time whilst at uni but I do know that the business agents are normally very knowledgable and skilled in what they do. In an age where times are hard and where businesses are becoming ever shrewd in how they spend their money, the business agents appear to still be valued.
The problem on a site such as this is that we are all interested in aviation, and quite often, wider travel/transportation. Thats why we enjoy making our own travel plans, tailoring it so that we can catch the A380 etc etc but your average employee usually couldn't give a toss, let alone be asked by their employer to search for the best deals themselves. And thats where much of the misinterpretation lies. Business travel isn't just restricted to businessmen/women and executives but the wider workforce including blue collar workers. Employing someone internally to search and book travel might well be an option but probably just as, if not more, expensive than using an agency. Plus, as someone else has mentioned, agents usually add value purely for being there when things go tits up. Easyjet has also benefitted from selling through business agents, it's model once being dead set against such practice.
So yes, you might get an agent who doesn't know there is a bridge between Sweeden and Denmark and you might get the odd one who is so focused on incentive rather than requirements (the actual Agent wouldn't endorse such practice as ultimately they lost a sale regardless) but by and large I would hazard a guess that they do provide value due to the fact they are seen as providing a valuable service by the business world.