The bribery charges aren't about payments to FIFA, they are about payments (for instance) that constitute fraud against FIFA (and various other subordinate soccer organizations, among others) as an organization. [0] In some cases, these are frauds that were being investigated when the relevant officials resigned from FIFA (ending the FIFA investigations, but not retroactively negating the fraud.)
While organizations current executives may have power over the organization, they aren't legally indistinguishable from the organization.
> Can't believe Blatter and his cronies would be so stupid
Its not uncommon for powerful people with a tendency to corruption to be, or become after years of smaller transgressions not seeming to have consequences, arrogant enough to commit major transgressions that authorities are willing and able to prosecute.
[0] https://s3.amazonaws.com/s3.documentcloud.org/documents/2088...
Well, the "end" is hard to assess. What has happened so far is a series of investigations begun and dropped over various sex-related crimes until the current set for "aggravated pimping" for which he was tried this past February with the verdict to be read in June.
Can't believe Blatter and his cronies would be so stupid, but perhaps some of the weaker and greedier executives were, so Blatter is happy to serve them up?