OK, let's go through your questions one by one.
Why are there 9 nav points for ever mission I choose?
Because at the beginning of the game you are in the Troy system, which always has 9 nav points. You will continue to launch in this system until you buy a jump drive and jump into another system, which has different nav points and bases.
Why do I run into jump points if I can't jump yet?
The jump points are always visible so you know where they are, but you can't use them until you buy a jump drive (and press J while in a jump point). Some people may not like the fact that you can always see them, but i think it is useful if you are fighting and want to quickly jump out and are looking for the jump point.
Where am I supposed to go?
Privateer is not like the other wing commander games as in there is no one fixed path you must follow. You go wherever your current mission takes you, whether that is out-system or not. But if you are talking about getting onto the story missions, then you must jump to New Detroit and talk to a fixer there to get started.
Which nav point is my base and how do I land on it?
Again, privateer is not like the other wing commander games. There is no one base which is YOUR base. Just go to where you are required to go during a mission. To land on a base you just have to fly close enough to it and you will land automatically.
Every choice in the communications menu seems useless.
The communications may seem useless just because you are used to people always responding to you in the other WC games, but they do work in privateer. You can actually use the comms to sweet talk an enemy into not attacking you (but you have to be persistent) and you need them during some story missions.
Why can't I eject if I just want to end a mission?
I don't think you can eject in privateer. I may be wrong but I have never ejected myself. You can, however, eject your crago. I think you press CTRL+X.
Why do the graphics look worse than WC1?
Actually, the graphics are supposed to better than WC1. I believe the bitmaps used in privateer are higher quality. This just depends on your opinion. I personally prefer privateer's graphics, but others may think otherwise.
Why is the game so choppy?
I'm afraid I can't answer this. The game obviously isn't meant to be choppy, but there must be something about your system that privateer doesn't like. Maybe you could tell us how you are running privateer? Are you using DOSbox in winXP or running it from win9x/ME? Or are you running it in real DOS?
Why is the view from your first ship so small?
Your first ship, the tarsus, is the worst ship in the game and you should upgrade as soon as possible. The ships you can buy in privateer are not miltary ships, so the visibilty is poorer than usual. The only dedicated fighter you can buy is the Centurion, so if you want better visibilty, save up 200,000 credits to buy one.