can cooperative society charge transfer fee for transfer by way of gift deed to family members

Yes.  Transfer fees may be collected by the society.

Since the Society is concerned with transfer of share in the name of titleholder (donee in the instant case) there is no such provision to charge any transfer fees in any of the State Cooperative Soceities Act, if I am not wrong.

It would be better to consult a local prudent lawyer as local (State) laws apply in the instant case

The transfer fee is based on the agreement between the residents and is incorporated in bye laws of the society if it is approved in AGM that limit prevails on any clause in the apartment act.

In which State are you?  In Maharashtra the Society can collect a tranfer premium from the transferor. Once upon a time it was Rs.25000/- I do not know how much it is now. If the transfer is to a close relative, no transfer premium can be charged.