Many games cheat and make the openings
artificially wide so that you can see the floor in the doorway instead of bothering with getting the size of the door correct. Some don't even bother with the concept of side-wall height and just have the doors be a simple break in the top of the wall, no indication of wall height. Many other games just don't bother with east/west doors at all, and instead just have north/south doors linked up by wide east/west hallways (e.g. Sword of Mana's Vinquette Hall), and it's a convention most players don't mind by now.
If you don't want to do "cheat" like that, consider having lighter wood in the doorway, lighter at the bottom (where the floor reflects light most strongly at it) and darker towards the top, and perhaps some special tiles to draw attention to that area by giving it a more interesting shape (door frame, hinges, decoration, etc).
In general, you should rely mainly on things like silhouette, floor patterns*, open doors, other decoration, and light shining through the doorway to show the door is here. You might even benefit from not having the top of the door indicated with the break in the wall, since it's a distracting visual element that doesn't correspond to the walkable part of the door.
* By having floor patterns that cross the doorway (lengthy carpets joining rooms, continuous floor texture instead of borders like at other walls, etc), you can subconsciously hint that the rooms are linked in that area, so the player doens't even "see" the wall between them.
An unrelated thing: Your walls feel very flat because the wood is perfectly aligned with the stone and plaster/daub, looking more like a wallpaper with those things drawn on rather than actual structure. Letting them stick out would help with that. You don't have to break tile boundaries, you could have a couple of pixels of wood/dirt/dark-dust at the bottom of the stone or something like that.
Here's a fairly minor edit:
I gave the walls a bit more volume by raising the stones a couple of pixels, and added sticky-outy bits at the bottoms of each pillar. Those same sticky-outy bits are visible around doors. I made the rugs less brown (so they don't blend visually with the walls; they don't have to be lighter, I just used the available non-brown colours) and extended them so that they look more like rugs laid between rooms, rather than just something attached to walls. In the back room, I also "opened" the door. I got rid of the tops of the doors, since they weren't conveying useful information imho, and were just "lying" about where the door is.
This is still not as clear as the north/south doors, but I think it reads better than before, at least to me.
Something missing from my edit is a distinctive visual element for the doors. For example, what if all the doors had little awnings, or some sort of supports, or other bits that stick out and look similar in both front and side view? Those would help a lot.