From what I can see as an outsider the main problems with the deal are as follows:
(i) The pilots took a pay cut when BA was struggling but now that the airline is performing well financially the pay cut hasn't been repaid after being adjusted for inflation.
(ii) The proposed deal is supposedly in-line with inflation, however unspecified productivity demands labelled as "management changes" are being made of pilots which could affect the pilots' quality of life/fatigue. Productivity related pay increases should be discussed over and above the inflation part of a pay deal when things are going well and it should be specified exactly what these productivity changes are.
(iii) There doesn't seem to be any inflation lock on the proposed deal, at least where I work pay deals take the form of "RPI +x%" or "£x or RPI whichever is greater", so if inflation rose, pilots would still be out of pocket.
(iv) General dissatisfaction at large with the way the airline is being run, especially regarding rostering and accomodation.
It may be true that BA isn't a workers co-operative, however that's one of the main reasons why trade unions were formed, to strengthen the workers' position in negotiations with the forces of capital. The capital/labour relationship is a two-way one, without labour capital doesn't develop and without capital, there is no-one to employ the labour force.