I asked my dealer the same question when I was initially looking and his response was differentiation. The base 3's (318 & 320) don't have the nav standard, the 328 has the business and the 335 has the pro - it's a clear step up and it allows the dealer to use the "do you want fries with that approach". I mean you _could_ buy the 328i and pay to upgrade the nav, but why not just buy the 335i and get the pro nav, the bigger engine and a whole load of other features standard. It's a pretty typical sales gimmick.
The same could be said for why some 3s don't have Nav as standard but all 5s do - it's just another point of differentiation to say why this car is a step up from that car.
When I was looking for my new car, I briefly looked at what Volkswagen had on offer and I considered both the Passat and the CC. The dealer showed me that you could option up the Passat to have _all_ of the features of a base CC (except the body shape of course) and it was still $6k cheaper. It almost seemed silly having two different cars but then the CC had additional options that the Passat didn't.
I sort of lucked out on the Nav myself. I was originally going to go with the Business Nav, and when I placed my order, I asked for Lane Departure Warning and was told that I needed to add Anti-Glare Side Mirrors. I did this and accepted the discounted price, though when I looked further in to it, I found that the Lane Change Warning, not the Lane Departure Warning needed the Anti-Glare mirrors. My dealer had ordered the wrong system. We got it fixed up and removed the mirrors, but the car was now $670 cheaper and the dealer wanted to redo the discount.
Since I'd already accepted the original price and organised finance, I noticed that the Pro Nav was about $1k more than the Business, but that the Lane Departure Warning was about $300 cheaper when fitted in concert with the Pro Nav. I ended up paying an extra ~$50 to upgrade to the Pro Nav and ended up adding Internet Connectivity as well. Because of the screw around I had gotten and the fact that it delayed my order, the business manager at my dealer ended up giving me the latter free.
320d Luxury, Sapphire Black, Black Dakota, Music I/F, Pro Nav, Ext Connect, Sunroof, HUD, Lane Dep Warning, Rear Cam, Internet.