It can happen many a times that a user with even lesser reputation can have a really valuable point/counter question to add, but it may not be complete in itself or simply might not be able to answer the question satisfactorily. In such a condition the valuable addition may be missed out.
It can happen many a times that there will be someone who doesn't do physics or care at all about it, but they have this website www.X.com that they want to promote, and having a bunch of links pointing from physics.se to X.com will help convince Google that their site is trustworthy (because this site is highly ranked by Google), so they will make a bunch of sockpuppet accounts and try to post a bunch of comments linking to their site.
Those comments get very annoying very fast, and they represent a huge source of wear on how this site looks and feels to search engines, casual visitors, new users, and established members. They are not something we want around. The reputation limits are there to keep them out, and they do an excellent job of keeping out the flood of harmful comments that try to get posted here. The fact that some people with worthwhile things to add are prevented from doing so by this system is unfortunate, but it's an uneasy compromise that allows us to have a high-quality site to comment on in the first place.
Generally speaking, the systems in place for protecting against spam are run by Stack Exchange itself, and not by the Physics SE site's community. This meta site is primarily for community issues and for software issues which affect this site only. Questions and proposals about features that are common to the entire Stack Exchange system should be raised on Meta Stack Exchange. (And, if you're going to post there, you should do your due diligence and search for the existing threads, like this one and the links therein, if you don't want them to close your question as an exact duplicate.)