If you have a large or medium size ship (Beluga, Anaconda, Python) and find a good location where you can stack passengers going to the same spot, transport missions can be very lucrative indeed, even after the bulk-passenger nerf (I use a mixture of economy, first and business class cabins).
If you’re happy to take a slow and steady approach, sight-seeing trips are also fairly lucrative in a smaller ship with a decent jump range. I made my first billion between this and exploration data in my Asp – took about 4 months of relaxed play. Pick a couple of locations and work on your local rep. Your explorer rank also contributes. I’ve had sight-seeing missions that offer as much as 15 million for a 3 or 4 stop trip, which usually take about 30-40 minutes in my Asp.
I agree that the financial rewards for long-range trips are comparatively low, but they often take you to some great spots. I’ve had some of my most enjoyable sessions in Elite taking scientists to some far-flung, exotic location (once I've actually got there!). If you take the time to collect exploration data along the way the rewards are pretty good, but that’s almost besides the point. Discovering a few "firsts" is a nice bonus as well. Depends on what you enjoy of course.