Real life has got nothing to do with color use. We study from real life, but we don't necessarily apply the same rules or we'd have missed artists like Van Gogh and Picasso.

There's no better way to represent a Torii gate than the tasteful use of bright red. I agree some more contrasting and shadowing would work, but leave the saturation be. It's spot on.

Like this the way it is, These things are iconically bright red. =)

I think you will notice that things aren't usually (almost) purely saturated all the way over IRL. The same image at ~96% saturation.
Yes, my edit's colours aren't neccecarily the best and maybe I did put the saturation down maybe a bit too much, but it's just an example of what could be done.I don't see why someone should restrict themselves to 1/36000th of the colour spectrum.

Why is everyone on PJ so scared by saturation. This picture has a lovely vivid red and your edit is like a muddy purplish tone.

Good job for your first piece of pixel art =D, an interesting perspective too. But there are quite a few things that could be improved here:

Maybe try to lower the saturation a bit and try some hue shifting. You don't need this many colours. and if you are going to use a lot of colours you should try AAing some parts, as some of it seems a bit jaggy. Also make sure your light source is consistent.

I made a bit of an edit for you (I managed to cut the colours down to 6 in my edit)

 Good one. Although looks a bit plain, maybe dithering could make it look better. The right collumn's base (left to us) should be fixed a bit.
 I belive you could have cut at least 2 colors, like removing the brightest and darkest colors, that are not much needed i would say. The darkest color is not needed in my opinion and the lightest it too bright. This is just my opinion.
 Keep it up.

I forgot to mention, there was a reference photography for this, which I no longer have. The image was not traced from it, though...

edit: the main information states this now. There is no longer any need for this notice, even though I can't delete it...