Amsterdam Train to Paris

High reservation fees??
If you book direct at www.thalys.com, you can often get advance fares for under 50 euros and no additional fees.

Thalys is a great train and, as Michael pointed out, advance economy fares don't cost a fortune. Consider that you'll be covering considerable ground as quickly as possible.

If you have a Eurail Pass, avoiding the Thalys is a bit of a slog. 9 hours and 4 train changes vs 3 1/2 hours and direct on the Thalys.
If you can pay for a reservation fee for a TGV, You can take the IC train direct from Amsterdam Centraal to Brussels Midi then change to TGV to Paris airport, then switch to the RER B into Paris, which costs 10 EUR not covered by Eurail Pass and it still takes 7 hours minimum.

If money is an issue forget the train and just fly from ORY on Transavia; I have found a flights 100 USD cheaper than taking the train and you don't have to worry about watching your luggage on the train as it makes stops with people getting on an off.
And in the case when I flew Amsterdam to Paris, I really wanted to take the train so I could show my uncle who had never been to Europe how great train service is there compared to here.

I have found a flights 100 USD cheaper than taking the train

Say what?????
The typical fare for most Thalys journeys is already under fifty euros. There is no way flying would be cheaper.

It looks like Thalys Amsterdam> Paris is running about 35€ - 54 € - 71 € adult fare depending on how far in advance you're able to purchase. The price issue comes in if you're trying to purchase for a train within the next couple of weeks as all the economy tickets are sold out. That's sort of par for the course regarding rail fares: the farther out you're able to book, the best chance you have of landing a price break. Cheapest trains tomorrow through the 16th look to be running 135€ or so.

Flying? It's possible one could find a good deal but you have to remember to add in transport fees to and from the airports, as they're almost always considerable distance from city centers, and any number of extra fees for luggage and whatnot that the budget carriers are so fond of these days. Those fees can escalate an advertised price in a fat hurry: read ALL the fine print. Again, if you hadn't planned ahead, the lowest fares are already likely to have sold out: Transavia isn't showing anything under 134€ (+ checked bag fees if exceeding carryon size/weight/number of pieces) for the next 4 days, and that one is only available tomorrow.

If you're booking a pass holder reservation, you can choose the cheaper 2nd-class reservation, even with a 1st-class pass. Prices are the same whether your pass covers France, or Benelux, or both.

If buying a regular ticket, then €135 is the full 2nd class ticket price for the direct Amsterdam-Paris Thalys train. Of course, 2nd class could also sell out on some departures.

For the line between Brussels and Paris, where Thalys has a monopoly, Thalys also operates a slower, cheaper IZY train: http://www.izy.com/, rail passes not accepted, fares from €19 in advance or €49 on short notice, also cheaper standing-room tickets.

Say what?????
The typical fare for most Thalys journeys is already under fifty euros. There is no way flying would be cheaper.

I tried to book a train Paris to Amsterdam during Xmas Holiday New years week 2016 less than a month in advance and the fare was more on Thalys than a flight on Transavia.

during Xmas Holiday New years week 2016 less than a month in advance

That says it all.