Take the Netherlands. From what I know, we pay more to the EU than we receive in subsidies and stuff, and hopefully trade is making up for that (who knows).
Take Spain. If I remember correctly, they're getting more from the EU than they pay, so for them it's a definite win.
So if the leaders from these countries go and negotiate, what's fair? Should we share all our wealth next month with the rest of Europe? Sounds unfair towards us. Should we keep it all and not invest in the EU? Also not a great idea.
Every penny we pay will make us more unhappy; yet every penny we don't share will make the other party more unhappy. I'm not sure there always are good outcomes. (This is probably one of the reasons why governments and politicians are fairly universally hated.)
A similar example could be constructed with the refugees issue. Some countries are being overrun; others only receive as many as those front-line countries send through. The front-line countries want to send as many as possible; we want to get as few as possible. Every extra refugee makes our representatives less happy about the deal and every refugee less makes them less happy about the deal.
I'd bet that especially for a country that thrives on trade that a definite win. Just think about the ports of Amsterdam and Rotterdam which serve as huge gateways for goods into the EU. They'd loose large amounts of trade if those goods could not be forwarded tax and border-control free to Germany and France.
I guess it's hard to estimate how much Germany gains from being in the EU. We're an extremely export oriented country and a substantial chunk of our exports go to the EU. Those certainly benefit - and those certainly benefit if the rest of the EU does better, so we could consider at least parts of the net payments as an investment. There are also other gains that are possible only because of the european integration: We're actually starting to share military assets with you: Germany provides the armored component of your 43rd mechanized brigade, the 11 Luchtmobielen Brigade is partially integrated into the Division Schnelle Kräfte, the german Seebataillon is partially being integrated into the duch Korps Mariniers and there's a LOI that the two navies want to share your most beautiful JSS, the Karel Doorman. Even from a purely financial perspective, not having to keep watch on the pesky Dutch seems to be paying of ;).
A lot of staff for trade negotiations has been cut, a lot of special rules and regulations from bilateral agreements were folded into common EU regulations. Joint research gets much easier, a lot of student travel/study agreements are governed by EU law.
Jokes aside: I think that a lot of the benefits that the EU offers go beyond the pure monetary part. Being able to travel freely, being able to work where you want without begging for a work visa. The Good Friday agreement in Ireland that basically upholds the fiction of two separate states on Irish soil while still having common cross border agreements is mainly possible because the relevant rules are done at a supernational level. I consider the money that Germany - and by extension me - pays a solid investment - despite all the numerous flaws that the EU currently has.
"That agreement shall be negotiated in accordance with Article 218(3) of the Treaty on the Functioning of the European Union. It shall be concluded on behalf of the Union by the Council, acting by a qualified majority, after obtaining the consent of the European Parliament."
[1]: http://www.lisbon-treaty.org/wcm/the-lisbon-treaty/treaty-on...