That's only true if you're ignoring a great deal of context.
It would be like watching Age of Ultron and coming away thinking that the Hulk was a villain because of what Wanda made him do to Johannesburg. Superman would not be willingly serving Darkseid and Snyder didn't portray Batman as being faultless either. His version of Superman was also far from a government stooge, to the point fans actually complained about him being too disrespectful to the military.