Frankly, the illogical nature of the tech tree is one of the few major faults I see with Civ 5. I think it hasn't been that bad in a while. There were quite a few silly techs and unlockables in Civ 3, but nothing as bad as the more head-scratching examples in Civ 5. And Civ 4's tech tree was actually very logical and coherent, within reason - it's just a game, after all.
But, what can you do, Civ 5's more rigid structure and fewer techs, as well as much more specialised tech branches make it pretty much impossible to keep things logical while keeping the game rules as designed.
I still miss the brilliantly done and extensive Civ 4 tree, even though I consider Civ 5 to be a vastly superior game...