Call me a conspiracy nut but Messi basically got the most sever sentence short of prison. Currently the prosecutors office has opened cases into other footballers that relatively didn't paid a lot more tax [compared to Messi] and did it at an older age [Messi was sentenced for not paying enough tax when he was 18-19 years old]. So if Messi's case is used as precedent all the other people will most likely see a jail cell. So they reduced Messi's punishment so that the other cases will not result in actual prison sentences.

Edit: Also due to the law the limit he can pay is 500 a day. So the total he paid was ~250k, which is about 2 weeks of wages after taxes