Though I personally don't rummage thru peoples documents, and I don't see my screeners rummaging thru peoples documents...you apparently don't know anything about the "scope of our allowed duties".
File a complaint? About what? "The screener made me empty my pockets for secondary screening"? Though looking at someones travel documents may be unnecessary, it is hardly complaint worthy.
Reading a person's documents extends beyond the boundaries of the administrative search. If the SOP permits reading of personal documents, I would be surprised. Reading through documents can even taint the attorney-client privilege.
And the OP's concerns were more than just travel documents related to the flight. The TSO went through CC's and other cards as well.