I believe the correct route is to pick up the rent proceeds as income.  Mortgage interest and real estate taxes go on schedule A and any other expenses are just plain old lost.

And the income might be 1040 Page 1/Schedule 1 line as opposed to Schedule E.

Who is making the decision that rent is below FMV?  And how far is it?  Before taking away all the deductions (if Mom does not itemize) consider whether the rent is reasonable given having a reliable tenant who can maintain the property while it increases in value.  And is that really rent he is paying, or just reimbursement of some of her expenses?  

(Not that I'm defending parents who won't untie the apron strings.)