That a CV might be binned because of someone's union affiliation seems a little far-fetched - unless you state your membership on your CV, how would they know? That said, if you do put it down, you deserve to be binned for stupidity in general
It is worth remembering however, that UK employment law protects your right to belong to a union and not suffer because of that choice... Better in than out these days I reckon (and that's speaking as a member of 'management', allbeit not in aviation at the mo).