This phenomenon is not limited to comment flags. All types of flags are limited in number, including question, answer, comment and chat message flags.
In fact, pretty much everything is rate-limited here. It just doesn't make sense to do otherwise. Anything that is not rate-limited is vulnerable to attack and/or exploitation; if the opportunity is there, it is just a matter of time. So why even leave that door open?
Rate limiting is not a serious usability problem as long as the chosen limits are sufficiently high to enable normal use, while preventing exploitation of limited, shared resources. One of the site's founders, Jeff Atwood, blogged about the importance of rate limiting here.
Note that, as mentioned in the FAQ you linked, the number of flags increases over time. It is tied to several different variables, including reputation and how many of your flags have been marked "declined" (as opposed to "helpful"). The exact algorithm is intentionally unpublicized, but the point is to allow users most likely to be raising correct flags a little extra leeway to do what they do well.
But we still have to be careful not to remove the limits altogether, even for these "proven" users. Just because you're not a bot today doesn't mean you can't be one tomorrow if your account gets compromised. And unfortunately, a high reputation doesn't prevent someone from going on a rampage after having one too many of their questions closed.
Do you really find yourself running out of comment flags frequently? If so, that is a sign of one of two things. Either:
- you are spending way too much time on the site and need to get out more, or
- the baseline limit is set too low, and we need to consider raising it.