Having trouble with VBA macro that deletes autofiltered rows

Try this.

Sub DeleteRows()
Dim rng As Range

    '
    ' Delete Macro
    '

    '
    With ActiveSheet
        .Unprotect "BEC"

        .Range("$AJ$2:$AL$1000000").Autofilter Field:=1, Criteria1:="0"

        Set rng = .Range(.Range("AJ3"), .Range("AJ3").End(xlDown))

        On Error Resume Next
        rng.SpecialCells(xlCellTypeVisible).EntireRow.Delete
        On Error Goto 0

        .Range("$AJ$2:$AL$1000000").Autofilter Field:=1
        .Range("B4:B8").Select

        .Protect "BEC"
    End With

End Sub