I hate to defend the TSA but the implications of this document aren't as big a deal as you're claiming. The fact that terrorists are not currently 'actively plotting against aviation' is not the same as terrorists do not have the intent and capability to target aviation. It just means that as the time of that assessment the TSA (or whoever was doing their assessment) saw no evidence that there wasn't an ongoing plot or targeting against aviation.
So, for example, there are a whole lot of terrorist groups out there (AQAP, AQ Central, Chechen separatists, etc.) that have targeted aviation in the past AND appear to continue to have an intent to attack aviation BUT they may have other priorities at the moment causing them to focus their energies elsewhere. Broad security policy isn't something one can just flip on and off like a light switch so (I'd hope) decisions of what security measures to use can't rely solely on who's planning to attack a target right now but rather have to take into account who is likely to target aviation currently and in the near future.
I find the shoe nonsense just as ridiculous as you do but this isn't the 'smoking gun' it may appear to be.