These fines are rare and the amounts are comparatively small. €120MM is peanuts to the EU. The intention of the fines is not to make money but to discourage illegal behavior.
Specifically, EU fines represent about 3% of EU revenue. The funds from the fines may not be used until the fine has passed all chances of being overturned by courts, which can take up to 8 years.
Finally: the fines reduce EU funding from member countries by the same amount. Even if the member nations decided to subsequently give more money back to the EU, there is a cap on how much money the EU can take.
Specifically, EU fines represent about 3% of EU revenue. The funds from the fines may not be used until the fine has passed all chances of being overturned by courts, which can take up to 8 years.
Finally: the fines reduce EU funding from member countries by the same amount. Even if the member nations decided to subsequently give more money back to the EU, there is a cap on how much money the EU can take.