Within the law, employers pay what they must to attract the quality of staff that they need.
Many women take career breaks to raise families and continue to be the main homemaker after returning to work. They may value other aspects of employment over and above absolute pay.
Being able to take time off for a sick child, part time hours, no overnight travel etc., such that many women accept jobs that are well below their capabilities and employers have no trouble filling these positions with quality staff at the lower end of the wage scale.
In companies such as Flybe, until more than a small percentage of pilots are women, the pay gap is bound to be large between men an women as the latter are mainly cabin staff whereas the pilots are mostly men. It is clear that women and men should be paid the same for the same job. This was the case in the multinational I worked in after leaving the services.