Exactly so; when this expression is used, it is often because someone has suggested that something should be done with or to xxx, and the reply is 'no, you can't do that; xxx is there for a reason'. We do not necessarily know what the reason is.
'Let's move that table from under the window.' 'No, you can't do that, it's there for a reason'.
'Shall we ask him to move ?' 'No, he's there for a reason'