Atmos was removed from Prime if one doesn't pay its ad-free extra fee.

I pay for the ad-free. 

You're right. Same issue here. It was working before, but I can't tell when it stopped playing Atmos.

Are you sure that the selected video does support an atmos audio track for your audio language settings? And did the exactly same selected content play atmos before? Compared to other services there seems to be less atmos content on prime video. 

Sonos plays the format it is sent from the TV (if it supports it). You don’t specify what device you have, but lets assume it is one that supports Atmos.

You also haven’t specified the TV, or the source device, so hard to be more specific.

 Looked at several newer movies on Prime Video on a Firestick.  None of them showed, in the description, as being Dolby Atmos.  One of them was clearly Dolby Atmos on Apple TV on the same Firestick.

 The Verge confirms to get Atmos it’s $2.99 a month extra.

How long has it been like this?
Did it previously work and has just started recently?

I’ve found Amazon’s ability to show the right labels on content and the behaviour of the app on different platforms is often all over the place, even without the app updating. The Amazon app on my Sony Google TV and my Apple TV app regularly behave differently.

Sicario which is in my account, so shouldn’t be affected by the “pay again to remove ads” option, hasn’t played in HDR since they brought in the pay tier on either device even though it previously did. Other content will play in HDR without issues. 

@MoPac 

I think best would be to give us some examples of movies you tried. As said imo there’s not much atmos content on prime video at all, and also like @sigh told the same movie can be offered different on prime depending not only on subscription plan but also on the used hardware/ platform. 
And on the other hand the same movie mostly is offered with different audio track options on different streaming services. If it has atmos on AppleTV+ it doesn’t has to be in atmos too on prime video. 
Sometimes it feels like a lottery.

If you check the atmos test video in your FireTV settings and Atmos is shown during playback, you can be sure on hardware side everything is ok. 

I found one. I believe there were more Atmos titles in the past anyways.

Try Jackpot! in plain English, don't choose the English dialogue boost options.

 I checked the new Top Gun movie.  On Apple is showed Atmos in the description.  On Amazon there was no Atmos trademark in the Top Gun description.  Did not try playing either one as I own a digital copy on Apple that does play as Atmos shown on the Sonos app.

 None of the other very new movies listed on Amazon showed the Dolby Atmos trademark.  We are Prime members, but we don’t pay the $2.99 extra.