The Wings Over Scotland blog, run by Stuart Campbell, issued the remarks on the social media website Twitter after a speech at the Scottish Tory conference by Oliver Mundell on Saturday. Mr Mundell junior is an MSP in Dumfries-shire.
The blogger stated: "Oliver Mundell is the sort of public speaker that makes you wish his dad had embraced his homosexuality sooner."
Many observers inferred this to mean that Mundell junior would then not have been born.
Wings Over Scotland later insisted that the comments were not homophobic, but may have been offensive.
But the Scottish Secretary said: "This sort of behaviour has to be called out.
"We're not going to face down homophobia unless we call out people who practice it. I'm just pleased to see so much support for my stance."
Mr Mundell, who was married with three children, announced that he was gay just over a year ago.
Wing over Scotland refused to retract the comments in response to online criticism of the remark.
He tweeted: "I have no problem with offending Tories. There wasn't an ounce of homophobia in it, however."
The blogger also said the comments paled in comparison to Tory cuts to the disabled and poor in Scotland.
But Oliver Mundell branded the comments "absolutely disgusting and unacceptable."
"I get a lot of abuse online," he said.
"There are certain individuals you don't want to give oxygen to but sometimes comments people make just cross the line. For other families who have gone through similar situations comments like that make it more difficult for people to be who they are.
"I don't think that's the kind of Scotland anyone wants to live in."