There could be a few possibilities as to why Platform 9¾ is not on the Floo Network.
First, it is located in King's Cross station, which may not have any fireplaces built into it. When wizards connect a Muggle structure to the Floo Network, they use an already-existing fireplace (think when the Weasleys came to get Harry at the Dursleys and Arthur connected the Dursleys' fireplace to the Floo Network, but it was boarded up and like five Weasleys piled up behind the boarded up hearth; it's in Goblet of Fire, when the twins give Dudley the Tongue-Tonne Toffee). If King's Cross has no fireplaces, then it would be impossible to connect it to the Floo Network.
Second, JKR may have wanted to show a stark distinction between the Muggle world and the magical world, and having a physical barrier that only witches and wizards can cross via magic is a very significant way to cross. JKR has made it clear that the Wizarding world is Harry's refuge, his home, where his soul lives, and to show a tangible, physical barrier between the Muggle World and Harry's home is rather poignant.
Third, as far as Platform 9¾ being in the midst of Muggles, Stan Shunpike summed this issue up pretty nicely: "[Muggles]!" said Stan contemptuously. "Don' listen properly, do they? Don' look properly either. Never notice nuffink, they don'." (Prisoner of Azkaban - page 29 - US Hardcover)
Finally, as the Hogwarts Express is a train and needs to leave from a train station, it makes sense to house it (however magically hidden) at a large station where it might blend more easily, or simply go unnoticed. It would seem it likely has its own track that it doesn't share with any other train.
ETA: It's against the law, apparently, for Muggle fireplaces to be hooked up to the Floo Network, as Arthur Weasley tells it in Goblet of Fire:
"Er - yes - sorry about that," said Mr. Weasley, lowering his hand and looking over his shoulder at the blasted fireplace. "It's all my fault. It just didn't occur to me that we wouldn't be able to get out at the other end. I had your fireplace connected to the Floo Network, you see - just for an afternoon, you know, so we could get Harry. Muggle fireplaces aren't supposed to be connected, strictly speaking - but I've got a useful contact at the Floo Regulation Panel and he fixed it for me. I can put it right in a jiffy, though, don't worry. I'll light a fire to send the boys back, and then I can repair your fireplace before I Disapparate."
Goblet of Fire - chapter 4 - Back to the Burrow