Normally, if a pilot is on duty, his priority number 1 is to get out to his aircraft, be it to operate it or to travel on it to/from active duty. While security searches differ between airports with the experience being less pleasant at some than at others, the following is general knowledge too:
- Security staff is acting under their rules and orders. They are not allowed to bend them for individuals, however strongly they may demand this. Discussing with those at the coal face is pointless.
- Not submitting to the security search will cause major issues up to and including disciplinary ones from ones company, see SASlesses post.
- A delay caused at, not by security will draw curiosity from ones company as well.
If one feels inappropriately treated at security or wherever else, there are reporting channels that can be used and that every pilot knows. Such reports will in my experience be investigated and resolved one way or another. But initially, being polite and complying with the lawful requests of security personnel is the quickest and least troublesome way across their checkpoint. The freedom to roll ones eyes when airside is not infringed upon.
And - an ID is generally quickly pulled out and shown. Once, twice, thrice, You name it.
That is, if one has it at hand.