You're definitely building your distribution incorrectly.
From the Ren'Py launcher (latest version), select your project but don't click Build Distributions. Instead, click Web (Beta), then Build Web Application. This creates a directory with a bunch of stuff including a game.zip file.
Ignore everything else and upload the game.zip file. Correction: you need to upload the entire directory, packaged as a zip file.
The Build Distributions button is for building downloadable games, not web games.