Here is a way to make a redstone line along your minecart track so that you can choose to pass all stations:

The redstone line runs parallel along the minecart track. I will try to explain how to do it the best I can...
First at the terminus (butter minecart station), provide two buttons. The left one (right to direction of travel) stops all stations, while the right one (left to direction of travel) is non-stop. (The repeater bit is actually not absolutely needed here, but I will explain what it is below.)

The redstone wire can go up to 15 blocks starting with full power, so put a repeater (setting to 1 tick is enough) every 16 blocks to extend it. However I suspect it won't go beyond unloaded chunks? Even if it does, there will not be an easy way to reset it.
Therefore, I'll add a latch every few chunks (not tested but I think it can be more than 8). (And here's the main point of this answer.) The latch looks like this (Edit: simplified version at bottom):

And the underneath revealed:

Basically, the latch "locks" the redstone power state, so that it can keep its state even when the source chunk is unloaded. The detector rail sends a redstone signal to reset the latch.

For the station that you want to pass, just use the redstone line to power the powered rails. If the line is not powered you will be stopped at the station. Everything else is exactly the same.

If you want to be able to do this for the reversed trip, just copy the setup in the other side. Due to the redstone line being single-direction, you cannot simply reuse it.
Also, you will not be able to change from "non-stop" to "stop all stations" without taking the whole trip (as I said, the detector rails reset the latches). But the opposite is possible, i.e. you can change to non-stop in the middle of the trip by putting a button (or a trapped chest if you want a bigger target) and use it to power the redstone line.
Tested on Minecraft 1.5 with the station beyond 40 chunks (640 blocks), not long but definitely have exceeded the chunk loading distance).
Edit: (x2) Didn't realize that it can further be simplified a bit like this until I've posted the answer:
