The main reason was seen as the lack of decentralisation.
The problem is that most ordinary folks lack the necessarily political wordstock to make themselves clear, since most folks simply do not know about complex political ideas and how to phase them. Most folks where I live would not know what 'centralisation' means, let alone be able to parse that this is one of their main reasons for voting Leave. Not would they know what 'protectionism' is, but it's another reason they voted Leave. Nor do they know what 'federalisation' is, but it's a huge, huge reason why most folks voted Leave.
In short, we do not want anything to do with a centralised, federalised protection racket. We no not want a US of E. And that is, openly, what many MEPs want. This is what Guy Verhofstadt wants. It's behind their EU army, anthem, currency, court and trade laws.
Unfortunately, most ordinary folks lack this kind of political wordstock so they simply cannot make their points effectively.