It's meant to punish Microsoft for failing to comply with the ruling, rather than compensate other browser-makers for the users potentially lost.

Isn't this the primary difference between civil and criminal law? Additionally, isn't this a civil case? It would seem to me that the entire point of the trail would be to deal with the lost compensation/opportunity cost issue.

It's a high fine, but on the other hand, EU did not ask for much. I am sure MS will spend some more energy on implementing court orders in future.

I understand the premise of the fine, but how is this supposed to help the consumers and businesses who now have to foot the $50 bill per seat?

If MS raises its prices, it will weaken their market position - that's the punishment for their malbehavior.

By that logic no company should ever be fined as it hurts their users.

They probably made much more out of their previous monopoly anyway.