The First Minister lambasted the cross-community political organisation after its casting votes allowed Belfast City Council to reduce to 18 the number of days the emblem flies from the city hall.
Weeks of loyalist protest blocked roads and injured more than 100 police officers but violence has subsided in recent days.
Mr Robinson told Alliance MLA Chris Lyttle his party had changed a settled status quo in Belfast.
"I hope that he and his colleagues will reflect on this issue and recognise the damage that they have caused by aligning themselves with Sinn Fein and the SDLP on this issue," he said.
"I trust that the next time a vote of a similar character comes to any council that they will think of the consequences of their action rather than simply trying to cosy up to Sinn Fein and the SDLP."
The Alliance has argued that reducing the number of times the flag is hoisted to designated days is in line with many local authorities in Great Britain.
A party statement said: "This position best reflects the constitutional position of Northern Ireland as part of United Kingdom at the same time as respecting those Belfast citizens who do not see the Union flag as representing them. The flying of the Union flag on designated days is a sensible compromise that reflects Belfast's nature as a shared city."
Mr Robinson argued raising the flag on the city hall for 18 days of the year, while for another two council-controlled buildings it will not be put up at all, was not a compromise compared to the previous status quo of unfurling the emblem constantly on all three buildings.
Nationalists at Belfast City Council wanted the flag taken down altogether, but ultimately voted on December 3 for an Alliance proposal that it would fly on designated days like royal birthdays.