Both are not protected rights, the Constitution does not guarantee the right to air travel or the right to lousy airline snack food. By buying a ticket you are opting in to the security measures which you can read up on before your purchase. If you disagree, don't by a ticket and get there some other way.
If enough people disagreed with the security measures and opted out by refusing to fly you'd actually see more of a change than if people got violent at a security checkpoint. If violence occurs at the checkpoint people are going to think two things:
1. There are nutcases trying to get on planes, increase the security so I feel safe!
2. The security worked because the nutcase didn't get on the plane, it justifies the security so I'll willing submit!
Going nuts at the checkpoint will not further your cause in the slightest. Honestly, the best way to voice your disapproval is to opt out of the security by refusing to fly with the current regulations. The TSA gets a fee from each ticket. Refusing to fly deprives them of funding. Also, if enough people refuse to fly and the airlines start seeing their revenues drop because of security they'll start screaming that the government is killing their business. Similar to the bus boycotts its often best to vote with your wallets. This will have far more effect than a single person causing a scene at a checkpoint.
We're not talking about air travel, we're talking about the search itself. The fact that it takes place during air travel should not be relevant. If it were, then you could situationally infringe on any right, and therefore negate the very existence of the right at all. Either something is a right, or it is not. You cannot logically qualify a right. Yes, we do in practice, but in so doing we fail utterly.
Either a person is free from unreasonable searches, or they're not. Period.
Your views are a wonderful fantasy, but in the real world it does not work that way. Were the slaves freed by popular dissent? Did Hitler surrender power because of international sanctions? Did Nixon have a sudden hippy-love-in moment and release the tapes in the spirit of transparency? Change occurs when it's forced, not when it's wished for. People alter their actions when those actions cause them harm (or at least have the potential to cause them harm) more often than when they have a sudden change of heart.
More importantly, the core question is: is it moral to endure injustice until random forces coalesce to relieve it, rather than to take a stand against it no matter the cost. Put into action, do you turn over the slave to his life and wait for the law to free him? Do you hand over your gun and typewriter until the government willingly return them? Do you submit to unreasonable searches (or by refusing remove the possibility of pursuing life, liberty, and happiness)?
I say no. You obviously say yes, and that's your right. I will not be following you in this course however. I'd rather make agents and officials so mortally terrified for their safety that they refuse to implement the offensive policies.
"People should not be afraid of their government...governments should be afraid of the people."