While the comic raises some points about The Federation, it does get grating after a while and seems to offer absolutely no points showing the good things that they do, making them a strawman to beat upon.
The "government bad" theme in the Coldest Equations arc. Of course, when it comes to "government-sponsored technology", there's loads of evidence to support it; look up the Brewster F2A Buffalo, the M16 rifle, and the Bradley Fighting Vehicle(see The Pentagon Wars for the step-by-step design process of the last of these lemons) - all so horribly defective that there was only one possible buyer, one which not only bought countless numbers but asked for them to be built in the first place: The Government. In the case of the deathtrap shuttle? They asked for something cheap and environmentally friendly which could be built, maintained, and supplied solely by low-bid government contractors. Leave out the "cheap" and "environmentally friendly" parts and that's the design statement of NASA's Shuttle Transportation System.
The genocidal culture that gets nuked in the Kallifrax arc is a pretty obvious Expyof Iran. Eerily prescient if you consider ISIS.
What Might Have Been: The Federation arc was originally going to be a good deal longer, but the readers' complaints regarding some of the Author Tract tendencies led to a shortening of the story. Thus, the readers never got to see Babbage (Data) confronted about his creator's obvious shortcomings in the software and design departments, nor Lothario (Riker) getting a brief analysis of his sexual mores. (This was well after Riker had sex with a neuter...) To say nothing of the far-too-familiar-to-Trekkies argument regarding why Geordi needs a VISOR. Ironically, some readers believe they would have complained far less if the Author Tract had eventually moved on to these potentially-more-entertaining scenarios.