From my experience, having always used win bonuses, I've found their influence to be minimal. The past 3 seasons, I've increased them when I've been up against especially tricky opposition (they re now 2.5m for league & 5m for the league and cup) and noted the performances directly afterwards:

Cup...increased at Play-Off...lost 3-2 / increased at Play-Off...lost 2-1 / increased at Preliminary...lost 5-2.
CL...increased at Semi-Final...drew 0-0, won on pens / increased for Final...lost 3-0 / increased for final...drew 2-2, lost on pens.
League...increased for match 16...won 1-0 / increased for match 9...won 2-1 / increased for match 18...lost 4-1.

This isn't definitive, by any means. It does increase motivation, but I've now backed myself into a corner where to put it up means losing large amounts of money and I won't be able to do that until my stadium's complete. I wonder if failing to increase it when going up a level adversely influences motivation? Probably not, but who knows?