This might be taking too scientific approach to a magical situation (and is not canonical and simply conjecture) but...
Consider your Muggle printer at home or in the office. Multiple people can queue up documents in the printer at the same time but that doesn't mean the printer prints them all out on the same page at the same time.
One could imagine that the Floo network implements some sort of buffering system as follows:
- An outgoing connection is initiated at the departure fireplace
- Traveller steps in to the fire
- Traveller states destination
- Traveller is absorbed in to the network (Floo) relay and a connection is established with the destination fireplace
- Traveller arrives at destination but is not ejected from the stream/network
- Floo network performs a check to see if the buffer is clear
- If the buffer is not clear, remain in buffer
- If buffer is clear, eject traveller from network
- If traveller is ejected, check buffer for additional travellers
- If the buffer is entirely empty, connection is terminated successfully
Just because the wizarding world does not rely on Muggle tech doesn't mean they don't employ logic or safe practices. When devising the Floo network (because presumably it was created by a witch/wizard and didn't simply exist) I'm fairly certain there was a team that sat down and hashed out these details beforehand. Although, I can imagine that the first tests of the Floo Network would probably have resulted in quite a few magical maladies such as the merging of multiple travellers.
Also, if it were me designing the Floo network I would probably increase the momentum at which the traveller entered the network so as to make sure they are ejected a minimum safe distance. Kind of like a little push from behind that makes you instinctively take a step forward to catch yourself.
Finally, there is probably a bit of unspoken/unwritten Floo etiquette involved too. Like a Muggle escalator, you can get to the top/bottom and just stand there forcing all the people behind you in to you and causing a pile up, or you can step forward or to the side so others can get past. That is, of course, if you have space to do so!
Again, all of the above is purely conjecture and reasoning, no canon here I'm afraid! We are just going to have to wait and see if Pottermore releases a technical specification of the network! :D