There weren't federal warrants under his name. I believe he was named in an application for a warrant against someone else—an application filed by the (ousted) LA County sheriff as part of what appeared to be a corrupt investigation of the sheriff's political opponents.

The more-legitimate criticism was that the nominee had little technical experience in aviation. It's not obvious how vital that is—the administrator of the FAA runs a massive bureaucracy; he's not testing aircraft—but there's a valid criticism that the administrator should at least be fluent in the lingo and able to question the technical staff. Especially at a time like now, when people are worried about the safety of the air system.