"We need to sacrifice convenience to gain security and freedom" is NOT the same as saying "Increasing security and freedom involves a necessary reduction in convenience." (Assuming, of course, that you lack the ability to simply throw resources at the issue.)
There is nothing that says that, in and of itself, making a system less convenient automagically makes it more free and more secure. In this respect it is no different than "good, fast or cheap" - intentionally making a craptastic product does not mean that it was faster or cheaper than a comparable product.
On the other hand, if you ramp up the freedom AND security of a travel system, it does become less convenient, because of the time that it takes to screen out the false positives and the false negatives involved in travel to sketchy places. If the bomb plot had not panned out, someone who was expecting their printer would be wondering where it is right about now.
I likely could conceptualize a system that would allow any or everyone, to travel between any two points on the globe with little to no chance of being killed in a terrorist incident, using a security apparatus that was completely invisible, non-intrusive and non-time-consuming. It would be astronomically expensive. Given that fact, I have some trade-offs to make. The problem that you bring up is that I could effectively make poor trade-offs, and gain nothing in return - the system could restrict who can travel and where they can go; it could still allow for terrorists to rack up an impressive body count; it could require time-consuming and invasive screening techniques; and, on top of all of that, it could still be ridiculously expensive. And a lack of any means to evaluate how effective the system is can exacerbate that.
BUT... that doesn't mean that the reverse is also true - that I could have the system be free, convenient and secure at a low cost.