The Merseyside outfit fell to a 2-1 defeat at Stamford Bridge, with Eto'o notching the winner with a close-range effort 11 minutes before the break.
Liverpool opened the scoring after just three minutes courtesy of Martin Skrtel's tap-in, a goal that came about when the visitors were awarded a free-kick for Eto'o's high tackle on Henderson.
Chelsea recovered from their early deficit to move ahead before half-time thanks to Eden Hazard's sublime curling effort in the 17th minute and Eto'o's third Premier League goal.
However, Rodgers believes the Cameroonian should not have been on the pitch at that stage, though he refused to criticise referee Howard Webb.
"I know we scored from it, but that was a wild challenge where he's (Eto'o's) raked down his (Henderson's) knee and shin and didn't even get a yellow card," the Northern Irishman said.
"He never even got booked for that, but he's a top referee Howard - he's a world-class referee."
Liverpool pushed for an equaliser in the second half, and were perhaps unlucky not have been awarded a penalty in the closing stages when Eto'o cut across Luis Suarez in the box as the Uruguayan chased down Cesar Azpilicueta.
Chelsea manager Jose Mourinho claimed Suarez was attempting to "provoke" the challenge, but Rodgers believes that is an inevitable consequence of Suarez's talent and feels a spot-kick should have been awarded.
"Luis will always provoke a challenge in the box because he's world class, where he doesn't expect to provoke a challenge is where he's challenged by someone who's not involved in the contact," he added.
"If you watch it again, he's running to challenge Azpilicueta. Eto'o is street wise and cute and blocks him, on another day you get that because it's a challenge in the area."
Rodgers also confirmed defender Mamadou Sakho is set for a spell on the sidelines after he suffered a hamstring injury late in the game, while Joe Allen will also be assessed after being withdrawn due to an abductor issue.
