What you're seeing in the current build is a change that's mid-implementation. Since the introduction of the guild system in Cataclysm, the nature of guild leveling and guild perks has shifted from being a reward for dedication and collective effort, to effectively being a penalty and barrier to entry for new guilds. We've made it easier to level guilds over the years, allowing low-level quests to count fully towards guild experience, and removing weekly caps on progress. That helps ease the barriers, but it's more of a band-aid than a true solution to the underlying problem.
Our current plan for Warlords is to effectively remove guild leveling (you could also think of it as "all guilds are automatically level 25"). We originally came up with two dozen perks in order to offer something at every guild level, but without the continued need for that granularity, we can streamline the system a bit. Many perks can just be rolled into default behaviors, since a majority of players already had them and the world was designed and tuned around their existence: Flight path taxis can just inherently move 25% faster instead of requiring "Ride Like the Wind"; Honor rewards and item costs can be balanced as if you had "Honorable Mention"; and so forth. For most players, who are in max-level guilds, nothing should perceptibly change.
We still want to incentivize guild membership, aside from the social benefits, so we're keeping conveniences like faster mount speed, instant guild mail, Mass Resurrection, etc., as exclusive benefits to all guilded players. The guild achievement system, and unlocked items and other benefits through completion of guild achievements, will remain as-is. We'd like to emphasize that system a bit more as a yardstick for collective accomplishment, rather than guild level which primarily just reflects individual effort.
The Cash Flow perk is obviously popular, though in most guilds it actually contributes less gold to the guild bank than something like Guild Challenges, since it only applies to looted coins. However, it also fuels some degenerate player behavior: if you've made an alt lately, you've probably noticed that you can't go more than a minute or two without receiving a guild invite - typically from "leaders" who are looking to recruit armies of often-unwitting players to both level guilds for later sale, and to increase the amount of Cash Flow gold that is siphoned into coffers to which only they have access. It can be a meaningful amount of gold for one player's pockets, but for something like a raiding guild, Cash Flow gold barely makes a dent in something like total repair costs. We're removing the Cash Flow perk in Warlords.
We do recognize that it's essential for guilds to have ways of financing their costs, and we will offer alternative, and more lucrative, options for doing so in Warlords (for example, bringing back some Bind on Equip epic drops in raids).
You cannot currently roll an alt in this game without being immediately spammed by random guild invites and whispers from people looking to have players join their guild. While some of these guild invitations could arguably be "legitimate," many of them are nothing more than farming schemes for players to gather gold, level guilds, and then sell the guilds -- perks, players and all -- off to the highest bidder. Will the removal of Cash Flow deter this behavior? That's a really good question, and I'm sure we won't see the results until Warlords
For most guilds, this really won't be an issue, because Cash Flow contributes very little to a guild bank's coffers unless you have a lot of players looting a lot of creatures for gold. From what I've experienced, Cash Flow will generate a tremendous amount of gold at the onset of an expansion as everyone levels, and then peter off to almost nothing once everyone has hit max level and stops doing quests on a daily basis. Watcher did, however, hop on Twitter to address the potential loss of guild income for smaller guilds that don't necessarily partake in raid content.
As Watcher stated, Blizzard is currently looking into other ways for guilds to generate gold -- whether it be via BoE epic drops in raids, or changes to Guild Challenges and increased income from other group activities. Cash Flow might be going away, but the ability to meaningfully generate some sort of guild income is something that is still very much in the cards and planned. What it will look like in Warlords
remains to be seen, but we'll likely have a better picture of it as the beta continues to open up with more updates.