For the same reason the GPLv2 has nothing to say about patents, even though patents are used to do the kinds of things the GPL was meant to prevent.
The thing to keep in mind is that the changes that web companies make to free software are not usually for internal consumption. The changes are user-facing -- but the software is delivered via the web, rather than distributed to the users, and so the web company never triggers any requirement to make their changes available. The GPL does allow this, but it is not in the spirit of the GPL, and the Affero GPL was created to deal with this problem.
I'm not sure that's true (I'm not the most knowledgeable person when it comes to the exact specifics of the GPL). Without institutions protecting IP (like patents, trademarks, copyright) the GPL couldn't exist, it's just a hack on top of IP.
I agree that it's not in the spirit of the GPL, but they did explicitly not add in sections about that in the GPLv3. The v2 FAQ mentioned that they were considering adding in web-based applications, but the v3 FAQ says it's still okay, but if you're writing software and want to make it not okay, use the AGPL.
The thing to keep in mind is that the changes that web companies make to free software are not usually for internal consumption. The changes are user-facing -- but the software is delivered via the web, rather than distributed to the users, and so the web company never triggers any requirement to make their changes available. The GPL does allow this, but it is not in the spirit of the GPL, and the Affero GPL was created to deal with this problem.