Tower Controller used LAHSO procedures unaware that the aircraft involved was operating under Part 135 contrary to published requirements.

Narrative

A C172 was VFR inbound from Approach. The aircraft called northeast and was told to enter left downwind Runway 9. We were landing Runway 9; departing Runway 35R and pattern traffic was on Runway 4. LAHSO was advertised on the ATIS. I had one Cessna in the pattern on Runway 4. I cleared the C172 to land Runway 9. The Cessna on 4 called in the crosswind to downwind turn and asked for a full stop. The C172 was about 1 mile out for Runway 9 and I cleared the Cessna for Runway 4 to land and instinctively given the operation for 4/9/35R issued a runway land and hold short of 9. Doing so inadvertently involved what I would learn was a Part 135 Air Taxi (the C172) which is a violation of the facility SOP for LAHSO which states that no Air Carrier or Air Taxi can be involved on either runway. I didn't immediately cancel the LAHSO for the Cessna on Runway 4 as I should; instead I continued to issue the traffic to the C172 landing on Runway 9. The C172 rolled out and began the back taxi before the other aircraft arrived making the LAHSO on Runway 4 unnecessary. Recommendation; just because the aircraft is a Cessna 172 doesn't mean it can't be an Air Taxi. I was unfamiliar with the call sign; but should of erred on the side of caution that LAHSO would not be permitted. Immediately after being relieved; I proceeded to review the LAHSO order 7110.118 as well as the SOP for LAHSO.