HOTD: Guess I'm just paying this one off

Three way limped pot to a 6c7cQd flop. I check from the SB, BB bets pot of .06, MP calls and I call with AcKcxx. Turn is 5c giving me the nut flush and I want to milk it a bit so I make it 1/2 pot and get called in twice. River leaves the board unpaired and I want to extract value from a presumed set in the BB so I only bet .08 into a .60 pot. Get a call from the BB then a shove from MP. I have half a stack left behind and his bet would put me all in. Ironically, there's really not a lot that I'm beating here. Villain's line is completely consistent with a straight flush and since I have Ac and Kc it makes it even more likely that I'm beat here since even the worst donks wouldn't raise with the third nut flush, they'd just call behind. Plus the flat call on the turn and shove on the river smells exactly like the nutter butters. Although I'm fairly sure I'm beat here I commit the rest of my stack anyway. BB folds and villain shows 8c9c for the straight flush as expected and the nut straight flush at that. I'm not sure how I feel about the call. I did consider that villain thought I may have been betting a set of 5s then slowed down on the river when the board didn't pair and he wanted to get paid for his flush but that still doesn't really fit the line for a 3rd nut flush or worse. It is possible that I called off half a stack because it is "only" 33 cents or that I did not give villain full credit because of the microstakes but I also think there is something to be said for folding when you are pretty sure you are behind.  The pot was giving me about 4.5:1 and I don't think that I'm right often enough in that exact spot for a call to be profitable long term.