As much as I would love to believe that UFO's are spacecraft driven by extraterrestrial creatures I have to say I find it hard to believe. I think we can prove without a doubt that there is no intelligent life in our solar system besides us. Why? If there was any intelligent life, I think that our array of probes and rovers that we have been sending to other planets would pique some sort of curiosity. Just as we can detect natural activities on other planets, I am sure that any other intelligent life could easily detect that these probes are coming from Earth, and would be eager to establish some sort of communication. If there is intelligent life outside of the solar system, there are two things we cannot assume. First we cannot assume that all intelligent life is necessarily much further along than us, and second we cannot assume that they don't face the same challenges for traveling long distances that we do.
For the sake of argument, lets assume that these spacecraft are alien in nature. Perhaps this civilization is only a hundred years more advanced then us, and perhaps they have just mastered the ability to send spacecraft to other planets far away using some yet unknown propulsion source. Perhaps again, that like humanity, these creatures are still in the phase of only having the ability to send probes to far off places, and that these things are being controlled remotely and not by an actual "pilot". This would explain why these things just fly around for awhile and then vanish, and always seem to be hovering over military installations and other places of interest. This would also explain why they haven't made contact, because in essence these objects wouldn't be able too.
It makes more sense though that these objects are the making of the world's armed forces. If you take a look at the time-line of most UFO sightings, the first huge wave is during the Cold War. Coincidence? This was also a period of time in which the US military would have been trying to use whatever technology that had to spy on the USSR, and of course would want to cover up any potential knowledge of their capabilities. It would also explain why the bulk of UFO sightings were over commercial or military installations, which obviously would be of interest to the opposition.
In conclusion, I would say that we have two explanations. Either these are some sort of military operations, that obviously would want to be kept secret, or there is some slightly more advanced civilization that wants to check us out, because honestly, what advanced civilization would want to explore earth? Seriously, the first planet we find like ours we probably will want to visit, the rest though, been there done that who cares? We have plenty of territory in our own solar system to exploit for material gain, and exploration to keep us occupied.
We don't know if these things are a security threat, whether it be a government project or an alien intrusion. Could we tell the difference? I believe that first contact will be made by astronomers or scientists, not the military, so I am not worried about it. I don't think this is an issue that we can really be kept in the dark about for too long anyway.