The stand-up said he was firmly for a Yes vote in next month's referendum but argued there were too many "cross-currents" in Scottish culture for it to happen.
In a wide-ranging conversation during the closing session of the Guardian Edinburgh International Television Festival, Boyle said he did not regret his most controversial jokes.
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During the State of the TV Nation event, he also attacked television channels for failing to take risks with their programming.
On Scottish independence, the comedian said: "I'm all for it. It won't happen. One of the reasons it won't happen is the media is just completely against it. There's a huge level of media bias.
"One of the reasons the BBC is biased against it that never gets mentioned is the BBC raises a licence fee of £300-odd million in Scotland - they won't release the actual figures but it's probably £320 million - and they spend, they say, £160 million, £60 million of which is very probably finessed.
"So it's probably a £200 million a year subsidy to the BBC."
He added: "There's just too many cross-currents in Scottish culture. One of the great things about being pro-independence is I get maybe half a dozen tweets a day telling me that I don't understand economics from Rangers fans."
Asked about the aftermath of a No vote, he said: "I think half the country will have had their dreams and hopes destroyed, so it will be pretty much business as usual for everybody."
He said he did not regret making controversial jokes about Katie Price's disabled son and the appearance of Olympic swimming champion Rebecca Adlington.
"Think of all the other things that we could get offended about rather than a joke that was told five years ago," he said.
In an attack on programming, he said that current TV guides look like "the entertainment programme on a f****** cruise ship".
He said: "There's a layer of people whose job it is to kind of reject things that are interesting. And the trouble is, that layer is at the top.
"If you have someone who's called a comedy commissioner, they should be allowed to commission comedy."
He added: "They [television channels] don't take any risks and they are taking less risks and they don't want to take risks.
"One of their priorities is not to take risks. They would rather not take risks than have falling ratings and they would rather not take risks than lose money.
"If they took some more risks they might hang on to some of their audience."
Boyle singled out the programming on Channel 4, which won the channel of the year prize at the festival.
He said: "They have a duty they have completely abandoned. They have tried to appeal to the absolute worst. It's the opposite of what their remit is.
"I don't think I would ever get anything on there because they don't want to do that kind of thing. Anything with any interest or excitement or edge to it."
Of the BBC he said: "I would cull a lot of their senior management and their pensions. I would get rid of a lot of hopeless people in there who are stopping good people from doing their job."
The comic also voiced his support for quotas to drive up the number of female comedians appearing on television panel shows.
He said: "It's just the wrong quota, make it 50/50.
"I like quotas because quotas put the responsibility on to broadcasters who have a lot of money, instead of on to comedians who are really struggling."