The defeat leaves Town without a win in their opening eight games.
Athlone Town remain rooted to the bottom of the League of Ireland's First Division.
Brandon Kavanagh scored twice as a youthful Shamrock Rovers' second team registered a 4-nil win against Athlone at Lissywollen on Friday night.
The defeat leaves Town without a win in their opening eight games of the season and manager Adrian Carbery says they didn't make things easy for themselves: