Why would Algernon want flowers? Something tells us he'd be just as happy with some tasty nibbles. When Algernon dies, Charlie tells us "I wept as I put a bunch of wild flowers on the grave" (258). Charlie sees the flowers as a symbolic act of remembering someone who might as well be a little blip on the radar. Algernon isn't some random mouse to Charlie, that's for sure, and we can't help but wonder who Charlie thinks will remember him when he's gone.
Charlie makes Alice go away before he completely regresses, so we know he wants her to remember him as an intelligent person. But he's only a couple of miles away from her at the end, back at the Warren School. In some ways, Algernon gets to be the stand-in for Charlie. Those flowers show that people care, even when they return to their normal lives and stop interacting with Charlie. As long as those flowers end up on the grave, that rascally mouse and his friend live on in memory.