On smaller beta sites, GL for example, people rarely hit their rep limit, but when they do, it seriously affects their rep. Why do small sits that don't have a Jon Skeet still have a limit? What good does it do them, and can it be removed?
What happens when the site graduates or otherwise grows? Do you apply the rep cap then or leave the site with no cap?
In the former case you are going to get lots and lots of complaints from people about the new restriction you've just applied.
In the latter case you have a site that is completely different to every other site in the network.
Most people don't break the rep cap every day - or even most days - so removing the cap won't actually benefit them at all.
Everyone on every other site in the network got their reputation with the rep cap in place, so it's not really a barrier to people using the site and contributing to the site.
If this were implemented it would cause far more problems that it would solve.