Several reasons, but Núñez, president of Barça from 1978 to 2000, was ultimately the one to blame.
The whole Ronaldo affair was trademark Núñez: buying a rising superstar from any league other than Serie A or England (very difficult to buy players from those two leagues at that time), but with a low (relatively) buy out clause (mistake); the superstar exceels and wants to renegotiate the contract (deservedly, 96-97 Ronaldo was Pelé/Maradona-like) + Núñez gets anxious and/or angry and incoherent (he favoured balance over "overpaid primadonnas") + another rich club steps in and pays the buy out clause + superstar leaves because Núñez still looks anxious and/or angry and probably will pay less than the new club (it was Inter, but it could have been AC, Juve or even Bayern, richer clubs at that time).
Núñez tried to save face claiming that Ronaldo acted like a mercenary whose agents were amoral and corrupt (they were corrupt), but the Barça fans were so angry that the loss of Ronaldo effectively marked the beginning of the end for Núñez (the shock was so big that a certain Joan Laporta created a group that openly opposed the aging/stubborn/cheap Núñez and tried a failed Vote of No Confidence against him.
Not even Rivaldo with two consecutive leagues could erase the memory of 96-97 Ronaldo and the huge expectations he created (especially with Cruyff gone). At least Maradona was an unpleasant little fella with a well-known cocaine addiction, and Romário genuinely wanted to leave in late 1994 and seemed like a lost cause for professional elite football (indiscipline, laziness, lack of motivation after the WC'94). But Ronaldo was young, a huge talent and liked the city/club. With Ronaldo still on board, Barça would have probably won the 97-98 UCL, and Barça fans knew it.
The moral of the story is that subsequent Barça presidents learned that some players are meant to be paid what they ask for, because they are that good. And don't mention Neymar, completely different stories: Ronaldo was not an immature man-child with daddy issues and Inter was not a state-backed club.
Ney's story is similar to Figo's: a mediocre president wasting away huge buy out clause money with rushed signings (Petit-Overmars, Cou-Dembélé)