First, if your planes are 98% full, then your prices are too low. Increase pricing 10%, see what happens. If your loads stay that full, increase another 5%, giving about a game month to settle between each boost. You'll run into issues over 30-40% most of the time.
Also, this thread can help you - http://www.airwaysim.com/forum/index.php/topic,57959.0.html
+1. You need to adjusrt prices. If your plane is 100% more than 2 days in the week, you could definitively earn more. At 98%, I'd go for +20%. On that line
. Unless you're on the crappiest seating setting, in which case I'd go up much slower, as advised by Schro. THere seems to be a limit above which LF drops drastically, and that seems to be lower with crappy seats.
Flying embraers on ~1000nm routes is somewhat marginal from a profitability perspective. Smaller jets/regionaljets are far better at closer in stuff as far as making money. Larger jets benefit in that they typically have a smaller cost per seat (but, overall, a higher cost per trip). So, if your options are filling 2x dailiy E190's vs 1x daily A321, you will make more profit by just flying a single A321...
...unless there is opposition. If my A148s begin to fly 2 daily flights against your lone A321, your profitability will plummet. You will still have(and I will probably have higher prices than you, meaning that you'll get 40 or even 50% of the traffick) some profitability, but not that much. While flying 2 E190s may dissuade me from entering the market.
So, an analysis of potiential opposition(both at home & at the target base) can be important in the choice. My A739 Flying between Glasgow & Belfast makes only trinkets because of the numerous opposing smaller planes. Unopposed, it would be near cheating in terms of income.