A source close to the Prime Minister said Mr Cameron thought the First Minister’s gesture “didn’t feel right, because it was a day for sport, not politics”.
The source suggested that, had Mr Cameron pulled out a Union flag, there would have been a furore.
The comments came after Mr Salmond revealed the flag was taken onto Centre Court in his wife Moira’s handbag. Large flags are banned by Wimbledon authorities.
The First Minister said he had “no idea” he would be sitting behind the Prime Minister and said the Wimbledon authorities had not minded his actions “in the slightest”.
Sources close to Mr Cameron also said he wants English ministers to start taking the message about keeping the UK together to their constituencies.
One source said there will be “English ministers spreading the word about the Union in English constituencies.
“There will always be Little Englanders – the Nigel Farage types – but you don’t have to scratch very far beneath the surface [of English people] to find a love for Scotland.”
It was also confirmed that Mr Cameron had spoken with Better Together chairman Alistair Darling a fortnight ago, and has also discussed the independence referendum with Labour leader Ed Miliband.
It is understood that the Prime Minister is so confident of victory he “wishes the referendum could be held tomorrow”.