A friend tells the following story. In 1999, he was watching Bayern Munich play Manchester United in a bar in Kiel, high up in the northern tip of Germany. Most of the people were drinking, chatting, playing cards – they barely looked up when Bayern took the lead. But when Manchester equalised in the 91st minute, a loud cheer went around the room. When the English team scored an unlikely winner two minutes later, people were in each others arms, singing, dancing on the tables.

Borussia Dortmund, Bayern's opponents this time around, may no longer be quite the romantic working-class club coach Jürgen Klopp tried to evoke in a Guardian interview during the week, but it's likely that his boys in yellow have the majority of neutral fans on their side tonight. For a vast majority, being raised as a football fan in Germany still means learning to hate Bayern.

Where does this animosity come from? There is their knack for scoring late goals, the legendary Bayerndusel – the German equivalent of "Fergie-time" – and their history of rapacious capitalism. My own team, St Pauli, may be known as the "buccaneers" of the German league, but Bayern actually has a history of acting like pirates: raiding smaller successful clubs for their best players and leaving them to sink into obscurity, like they did with poor FC Karlsruhe in the 90s.

But sport is only half the reason. Munich is not only the richest club in German football – Bavaria is also Germany's richest region. Federal Germany is a transfer union, and in 2011 Bavaria paid 3.6 billion euros to subsidise poorer parts of the country, such as Berlin. It has not always been thus: until 1986 Bayern used to be subsidised by regions in the industrial west (where Dortmund hail from), and two years later it became the first and only region to transform itself from "receiver" to a "giver". Nonetheless, no German politicians have been more vocally opposed to eurozone bailouts than those in the Bavarian CSU – its finance minister has loudly campaigned to have Greece chucked out of the euro.

There may be some unresolved psychological issues too. The first football chant every German child learns is the Freudian "Zieht den Bayern die Lederhosen aus": "Pull down the Bavarians' lederhosen". One reason why we want to see them stripped naked may be that they have strong belief in their distinct cultural identity. A separate kingdom until 1918, Bavarians have they have their own folk costumes, their own political party, their own culinary tradition, a small separatist movement, a bloody castle as their own embassy in Brussels and an annoying habit of belittling other Germans as Preissn, "Prussians". And yet, Bavaria's ongoing economic and sporting success seems to imply that that arrogance is not entirely unjustified. Which is, of course, precisely what the rest of Europe finds so dislikable about Germany.

Over the last ten years or so, Bayern Munich have got very good at convincing the rest of Germany that they are not that bad after all. In 2003, they organised a charity friendly to pull back St Pauli from the brink of bankruptcy, and loaned Borussia Dortmund 2 million euros when the club was on the brink of collapse. They have insisted on TV money being distributed according to league position, when they could earn a fortune if it was assigned on the basis of viewing figures. They looked after troubled players like Sebastian Deisler, when other clubs might have just cancelled their contracts. Most annoyingly of all, they started playing free-flowing, inspirational football. Bayern promised an answer to that much asked "German question": whether Europe's largest economy can be strong and powerful without being evil.

About a month ago, that answer became a bit more complicated. On 20 April, it was reported that Bayern's president Uli Hoeness, who has come to embody the club's brand of socially responsible enterprise, was investigated for tax fraud. Just after German politicians had spent weeks lecturing Cyprus on dabbling in irresponsible casino-capitalism, it emerged that the man at the centre of Germany's most successful football club had lost millions on stock market bets.

All this means that tonight's match at Wembley is at least as much about politics as about football. Shortly before the Hoeness scandal broke, conservative politicians had been lobbying for a tax amnesty deal with Switzerland – did they know about Hoeness's affairs? Hoeness has repeatedly expressed his admiration for the chancellor, and Merkel has had to confirm that she had met the Bayern president in private seven times in the last three years – now she is reportedly staying away from London today for fear of being photographed with him.

The Swiss tax deal collapsed partly because of opposition by her main rival in September's elections, the Social Democrat Peer Steinbrück – who is also happens to be on the supervisory board at Borussia Dortmund. Borussia, incidentally, is neo-Latin for "Prussia".

• Philip Oltermann is the author of Keeping Up With the Germans: A History of Anglo-German Encounters