Right now most of the EU budget is contributed to Brussels from member state governments, and there is no direct tax on EU citizens to pay for the bloc's administration. Taxpayers are already paying for the EU, but they do it through their taxes to the member state governments, which in turn then send money to Brussels. It would be as if in the US, you didn't pay any federal tax but only tax to your state, which then in turn sent a chunk of money to Washington each year.
What the commission may propose in September is to move some of that taxation directly to a transaction between the individual taxpayer and Brussels. It's still unclear what form this could take, but it could include an EU tax on luxury items, air travel or large financial transactions.