It's definitely not for credit card spend. That posts as WR points, and once you get enough WR points, you can convert to airline (or in this case rail) miles / points.

As to bonus points, most bonuses are separate for WR points vs miles (in this case actually rail points).

In fact, because you may lose out on WR points bonuses if you choose to earn Amtrak points directly, you should do the math, and see whether it really makes sense to earn Amtrak points directly, or whether it makes more sense to earn WR poitns and then later (once you've accumulated enough to convert) convert WR points to Amtrak points.