Answering my own question...
I found that with the master pages the controls are buries really deep. The Page contains 1 MasterPage control, which contains 4 additional controls, one of which is the Form control, which contains the Content Placeholder control which contains the elements I was looking for.
Here's my code:
Dim formControls As ControlCollection = Page.Controls(0).Controls(3).Controls(1).Controls
'page . master page . form . content . control collection
For Each control As Control In formControls
Makes perfect sense and now I understand how Page's are organized.