That is unfortunate. Can't you just simply change the permissions on those files?
If you don't have Linux on your computer, I think you can just boot into a Linux LiveCD and correct the permissions.
Meanwhile, I tried a few other games downloaded from ITCH.IO too, and it is very strange, but some of them have this exact same issues with permissions.
On the other hand, other native Linux games, like those I have on GOG or from Steam, never have any problems with permissions.
So it seems to be the problem not your fault!
I don't know how these things work, maybe it is somthing to do with ITCH.IO?
Or maybe the engine, the programming environment (sorry I don't know how it is called) those Linux games written, is responsible for this? Or maybe it is something to do with the Linux distro that I use? You know, there are lot of different Linux variants out there, lot of thigs are so different compared to other Linux, maybe on an other Linux this problem won't occures?
(I think I have an unused laptop somewhere, with different Linux istalled on it, so I can give it a try and see if that machine have this same issue. But, you removed the Linux download...)
I think you should keep the Linux version, please leave the download up, because -regardless of this problem- the games runs without any problem. And in my experience, this is a rare thing! Beacuse (sadly) ~50% of the Linux games I downloaded from here doesn't even work no matter what. They just simply doesn't work. But yours works perfectly after fixing those permissions.
So, how about keeping the Linux version, and simply write it in the descriptio, that on the Linux version maybe the user need to change the permissions. You know, more platform, more people can play your game.
And of course, I'm very happy that you considered what I wite about the gameplay. Keep up the work!