Operator Strathclyde Partnership for Transport (SPT) said it did not allow any political content in advertising.
A spokesman for SPT said the posters had "slipped through their net" and were deemed in breach of guidelines.
Stuart Campbell, who runs the Wings Over Scotland site, denied the posters themselves were political and accused SPT of suppressing debate.
An SPT spokesman said: "SPT advertising contract guidelines state that Subway sites should not be used to campaign or lobby for political benefit.
"Our advertising agency applies that standard to all commercial bookings but unfortunately this particular ad slipped through their net. The ad was taken down as a result."
Mr Campbell said he was "disappointed, but not exactly surprised" by the decision which he said had been made by an organisation "dominated by Glasgow Labour councillors".
He said: "The content of our website is political, but no more so than the numerous union-supporting newspapers the Subway does accept advertising from, and the advert itself made no political statements whatsoever.
"It simply advertised the site as a source of information."
Posters advertising pro-independence website Wings Over Scotland have been removed from the Glasgow subway system.