It goes back to the 1900's when Spain was ruled by General Franco, a military dictator who took power after the Spanish Civil War. Franco openly oppressed any language (and culture) other than Castilian Spanish. That meant that Catalan, the Spanish language spoken in Catalonia, Barcelona's region of Spain, was outlawed. The only place Catalans could speak it was in the Camp Nou, Barcelona's stadium. FC Barcelona was the people of Catalonia's way of rebelling against Franco, which led them to be viewed as the "rebellious" club, while Real Madrid is viewed as the "establishment" club. This fostered deep hatred between fans of Real Madrid and FC Barcelona, which is renewed twice a year when the two side contest El Clasico.
It should be noted that players of both clubs suffered equally under Franco's regime.
It doesn't help that a natural rivalry occurs from the geographic fact that Barcelona and Madrid are the largest cities in Spain.
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No way! Real Madrid and Barcelona hate each other because Real Madrid is in Spain and also based in Madrid and Barcelona is in Catalonia and also based in Barcelona! Madrid and Barcelona are the two biggest cities in Spain! So there is no way they would ever be friends!