Brundle said on the AUTOSPORT Stage with KX during AUTOSPORT International 2014 that the situation was more complicated than it appeared, but was definitely a worry.
"The main problem is that they've got to stop it being so expensive to run the cars, so it stops the need for all this cash," he said.
"When a team like Lotus, the only one to really challenge Red Bull consistently last year, is short of money then something is fundamentally wrong.
"One way or another, the racing's got to be paid for. Whether it's with Santander following [Fernando] Alonso around, or Vodafone when they had [Lewis] Hamilton and [Jenson] Button for the British market, somewhere it's got to be paid for.
"You can't go racing on fresh air and there's not enough coming in from the organization.
"There's no doubt that the pay drivers are creeping their way up the grid. But they're still great racing drivers. Don't think anybody who's paid to be there is not a high-level racing driver."
He emphasized that the pay driver tag could be deceptive.
"The balance is getting dangerously close to the pay drivers dominating," said Brundle.
"But it's an awful expression. It's a label that you just can't get rid of. Niki Lauda makes the point that he had to borrow money to pay for his early drives in Formula 1.
"I promised Ken Tyrrell Â£150,000 I just didn't have in 1984. I was just winging it. And eventually he said to me 'I know you don't have the money but I want you to drive for me anyway'.
"One way or another, you have to facilitate the money, so let's not get too hung up about it.
"But it's disappointing when you see a driver like Paul di Resta getting booted out of F1 when you know that others are in because they're bringing cash.
"That's the bit I'm getting uncomfortable with."
Brundle also believes that F1 needs to put more money into ensuring that the most talented drivers come through the junior series.
"The money doesn't find its way back into grass roots – or at least nowhere near enough of it," he said
"Somewhere like Wimbledon does put a very significant number of millions each year back into the system."