Please clarify obstruction question

[LIIRISHMAN]

This was a question posed by my association president earlier today.One out R1 is on 2nd base.Fly ball to outfield R1 leaves 2nd base at the crack of the bat.R1 is obstructed by the shortstop and is tagged out at 3rd base.Now if the umpire signaled obstruction and there was no appeal of the missed bag isn't she entitled to protection between 2nd and 3rd.I would have placed her on 3rd but I was told she was out. I didn't get any further replies why she was out but I'm asking here.