Gosh I love this quote :
"If is not a safety issue the capt can do anything he,she wants."
Ahem, this is the CRM forum!
As per the OP question, it really depends whether the Flight Deck is smoking or non-smoking. If it is permissable for the Flight Crew to smoke in there (are there still airlines out there that allow this?) then basically the other crew have to sit there, shut up and live with it. As much of a filthy, disgusting habit that it is, it is his/her right to smoke in that environment.
HOWEVER if the Flight Deck is non-smoking then the Captain is not abiding by SOPs and then this is an issue. By all means, address the issue to him/her directly before running off to management. Be aware that this direct approach may cause friction between the two of you and you may end up suffering the consequences of "speaking out of school" - however in the interests of good CRM then you must do so, and are perfectly entitled to! Make sure that it is followed up by the appropriate paperwork in order to get the issue addressed and reconciled.
The days of the Captain being this God-like figure are over. S/he is a professional in their field but is also human! Humans make errors in judgements, and a
good Captain will recognise this.
Best Wishes
SG
