We have looked at this game critically and found that we agree with your assessment that there is too much luck. Furthermore, the penalties and rewards for that luck are too extreme the way the rules were written.
DISCLAIMER: If you love Monopoly please stop reading this, you will love Boxcars. If you like games of strategy and planning, please continue reading.
This game is far too random, and doesn't offer as much as a viable means of strategy. Before I suggest to you possible alterations to the rules, we have to examine what's wrong with the game.
Too Much Luck
Random starting location, random destination, moving a random number of spaces each turn.
If you happen to be traveling on someone else's rail lines, and you roll low, you are getting penalized AT LEAST double. Moving slower means increased number of turns, which means other players are gaining an advantage on movement alone. Since you are not on your lines, you are paying the bank or other players more for your crappy roll. It's not only possible but extremely likely that on a trip covering more than 10 spaces you will spend more than you make for the trip.
Feels like Monopoly
Monopoly is a good board game when you were 8. The same reason why people wouldn't want to play Monopoly is why you don't want to play this game. You will randomly get muscled out and there will be nothing you can do about it. No strategy, no plan, nothing. Just hope you get stuck in jail so you don't have to pay some stupid high rent because you went 3 laps around the board before you ended on a property you could buy.
There are more things we find to be a bit off but here are some rules we've tried that make the game less brutal. Consider using any or all of these, we have yet to find the perfect combination of these rules that allows for maximum strategy in such a random game:
You pay for using someone else's lines once. Once you decide to use a line that's not yours, you pay that person a 1 time fee. As long as you remain on that same line, you do not pay again, whether that's 1 turn or 10 turns. If you junction off onto another line, even another of the same person's lines, you pay again. You pay at each junction (think of it as a connection fee). What this does is it allows you to plan a route, at least initially, taking advantage of longer lines or lines that you may own. It just adds a lot more strategy. Optional: You may wish to keep the $1k per roll on un-owned lines as a tax to the bank.
You get to see your next destination before purchasing a line. Normally you go to your destination, cash in, purchase route, then see where you are going. This way you can see where you are going and decide if you want to purchase any route in between where you are and where you are going.
Roll a random sector of the map, choose the city. Perhaps you are headed to the southeast, but are blocked out of Miami entirely. It might be more cost effective to go to Atlanta cause you have a way in there. You won't get paid as much, but it will cost you less. Maybe you own lines into Miami, and it would be worth your time to go farther. This helps getting totally screwed.
Roll 2 destinations, pick one. Still random but a little more forgiving.
"Contracts". At the start of the game you get your start location, then roll 3 random destinations. Write them down and you get to pick which one you go to. When reaching that destination cross it off and you MAY roll another. The catch is you have to complete all the contracts you take, so eventually you will have to decide to stop adding to your list. At soon as you have the required money, and all destinations complete, you can then return to your home city and attempt to win.
We find these rules to help, why let a $x game sit on the shelf and never get played because of bad rules.