Factual error: The film's plot violates the third of the Ten Immutable Laws of Security by Scott Culp. The premise of the law is: When one has physical access to a computer system, given enough time, he can take over the system. In the film, the reverse happens: Dane takes over an ATAC site remotely while people inside (who have complete physical access) cannot do anything to wrest the control back. In the real world, it is usually possible to simply cut the connection cable or antenna and take control back. (Even Windows XP and later have such simple lockdown provisions as part of Windows Firewall.) After the lockdown, the passcodes can be changed and other measures taken.
Suggested correction: They don't have physical access to the satellite. It is in orbit, it is impossible to have physical access unless they had someone on the satellite.
That would be a plausible explanation, had it been in the film. But in the film, Dane hacked into ATAC system, not the satellite. That's how he implemented bogus satellites.
You also have to remember Dane designed and wrote the software that ATAC is using. He may have written in access stuff that can't be disabled. So they couldn't have disconnected the building and gotten back control of their systems. There is no way that they could have gotten back control of their satellite.
An yet, the exact opposite happened at the end of the film: Ryback shot Dane's laptop, severing his persistent remote connection. Immediately, ATAC personnel regained control of the satellite. It appears you're smarter than the filmmakers and would make a better film if you tried. But it also appears that they've made not one but several mistakes here.
Other mistake: When Ryback enters his message about the train being hijacked into his PDA he faxes it to the Mile High Cafe and signs it Ryback. When the cook at the cafe gets the fax there is no signature on it.
Plot hole: Dane's motivation for hijacking the satellite is supposedly because ATAC fired him. But he would have already had the satellite programmed to respond if he used it remotely like he does on the train except he wouldn't have known he'd be fired at the time, so he'd have no reason to have the satellite ready to hijack.
Suggested correction: Dane was a paranoid genius. There's no way that he didn't build in a back door that he could take over the system remotely.