The merits of flight/duty/rest time regulation for both part 121 and 135 have been debated ad nauseum for long enough for me to be sure they won't be resolved to anyone's satisfaction any time soon. That said, commenting on a NPRM is allowed, and one could even say encouraged by the administrative rulemaking process in place within the USA.
As to the matter of whose comments will be given any notice or affect the outcome, that's another issue. Every American citizen should realize that our form of representative government relies upon blocs of influence to decide policy. As a consequence of this truth, those blocs of influence with the greatest resources usually affect the process outcome to a greater degree than those with fewer resources. A more cynical way of stating this dictum is that those with the gold make the rules.
In the 121 airline world, the airline corporate entities win most of the battles. Their only organized opponent in any governmental matter is the various airline unions, whose effectiveness at swaying the outcome of rulemaking over the last few decades is a matter best left to be debated on another forum.
In the 135 on demand charter world, charter and airplane management companies are represented in government affairs by a number of industry organizations. They do so virtually absent any organized opposition.
The well constructed reasoning of individual industry professionals commenting on NPRMs is a good thing, don't get me wrong. But providing facts and research supporting one's views is far more compelling and the only way for individuals to have any hope of influencing the outcomes sought by the better funded and better organized industry representation. In short, any comments made regarding the NPRM should connect the dots between the proposed rules and their effect upon aviation safety if enacted or are not enacted. Expect industry to present cost/benefit analysis which support a set of conclusions which are contrary to the typically expected viewpoints of flightcrew members.
This particular battle will be fought and won or lost, but the larger fight for sensible and balanced regulation will be a long one. There are many battles yet to be fought and incremental evolution rather than revolution is the realistic expectation. In other words, don't expect any big change at all. Expect industry to get most of what it wants, with a few concessions that appear to recognize the known facts and maybe make things that little bit safer.
In conclusion, let me add that the part 135 flight and duty time Aviation Rulemaking Committee submitted it's conclusions and adjourned back in about 2004 or so. The rules were successfully blocked by industry and have not been revisited since. The NPRM in question is limited to part 121 operations and has no regulatory effect upon part 135 ops. As far as part 135 on demand charter goes, things stay just the way that they are!