From Basel to Amsterdam, Train or Plane?

I would fly it is not that scenic and too long for my taste.
But you must be doing something wrong searching for sure as I see prices around $120
Thetrainline.com.

You are probably looking at the wrong website.

We rode the train from Amsterdam to Basel last summer. Once I land in Europe after the long flight, I like to stay on the ground. I dislike the whole airport procedure and waiting around, and you have to add the cost of the transport to and from the city at either end. On the train we can walk around, perhaps talk to other travelers, have a snack in the cafe car, and use our e-devices if we wish.

I bought our tickets on bahn.de about 3 months in advance. I could have paid €39,90 each for second class, but chose first class for €20 more. €119,80 total for two. As for scenery, it was not like the Alps, but certainly scenic enough, or at least interesting where not scenic.

This is a long journey to be doing by train, 7½ to 8 hours. Well over the time threshold where flying would be quicker.
If you hate flying (and I hate airports), and you have the time, then take the train. Otherwise fly.

"$500, . . . . Surely I'm doing something wrong? - You are almost certainly looking in the wrong place.
I would look for times and prices on the DB website: https://www.bahn.com/en/view/index.shtml
I looked at random dates in May, and got prices starting €39.90 per person.

You can either go north through Germany, via Frankfurt and Cologne, or via Strasbourg, Charles de Gaulle airport and Brussels.Do not take a route via Paris, that involves crossing Paris on the métro - not a good option.

By air Easyjet ( https://www.easyjet.com/en/ ) starts at CHF 31.69 (plus bag charges, and a few other things)

Both routes offer advance-purchase discounts but the route via Paris by TGV Lyria and Thalys trains is more expensive than a route via Germany on ICE and other trains.