Well... I go to very few places that charge cover, in fact, I will avoid bars the charge cover unless I am outvoted or no such place is available (many bars/clubs in Minneapolis do not charge cover, and I tend to avoid those).
Profit of liquor sales is actually even more lucrative for govenment than from cover charges. Part of the cost the bar has to pay for the alcohol is excise taxes paid to the federal and frequently state/local governments.
Therefore, if a waived cover charge is offset to the same profit by increased liquor sales, government is getting more money as they are collecting more liquor excise taxes and the same income taxes.