This is the isometric grid zoomed in and the pixels have been marked, the lines are made by two pixels of width and one of height, let's call these kind of lines horizontal lines and the pair of pixels from those lines bricks so they're easier to refer to in this tutorial

The perfect pixel lines

This star-looking group of lines is very basic and important
Just like a star it will guide you on the path to pixel art (liked that?)
They are the perfect pixel lines, even though they're jagged (or "pixelly"), they are as smooth a pixel art gets
You should try to use this kind of lines as much as possible but you will probably have to make exceptions (unless you want to use the style they use at eBoy, where everything looks like made of legos)

Here's an example of an irregular line. I'm sure you'll notice it's too jagged
Ideally, these kind of lines should be avoided.

I decided to make the roof bigger than the rest of the hut. Yes, it would have been easier if I had done that from the beggining but you might learn more with 
this.

I added two bricks to my top horizontal line, and from the ends of the top (red) line I drew the roof lines (blue) again. I recommend using color like I did, if you don't you will end up with a lot of black lines and it could get confusing.
Having the long blue lines, I decided where the roof would end and drew a green line to know where to cut the blue ones:

Take a look at the point where the green line meets the blue line, notice that the height where the green line meets the blue line has to be the same on both ends of the roof. So make a horizontal line from that point to the blue line on the other side of the roof to mark where that side should end.

Then from the point where the new line (in this case purple) meets the blue roof line you make another horizontal line to the other end in the same side of 
the roof.
and delete the unnecesary line ends

I cleaned up the old lines and unnecesary ones and made the colored lines back to black

A hut with a paper roof would suck so I copied the roof and colored it so the lines under it can't be seen (so I avoid the mess) and placed it two pixels above the original roof, and then I cleaned up the colors and corners.

THEN I decided it looked like a dog house so I made it longer by copying like half of the hut and placing it on top of itself but farther horizontaly
And drew the door and a window and to make the other window I took the first one and flipped it so that it would have the same size and height

And now we're getting somewere

Coloring!
there are lots of ways to color things in pixel art, but like I said before this is how "I" do things.
The color I chose is a lot like wood, nobody likes going blind so you should select custom colors that aren't too intense.

Now use different shades depending on where you want your lightsource to be. 
Mine is almost at noon so the roof has to be much lighter than the rest

This part is important. How to deal with the corners.

This little drawing should help you see how I deal with them. The corners that are "out" are much lighter than the rest of the object and the corners that are "in" are darker (but not black)
So that's what I did to the hut, except it doesn't have "in" corners but I made the door, window and roof outlines a little lighter.
The outline of the whole hut is still 100% black.

The windows are tricky, there are lots of way to make them. One of the best ones is probably when you can see the interior of the place but that one's hard.
I don't know what's the best way, my windows usually look different all the time so they're up to you.
I'm pleased with the style I used on the hut's though

(note the small bevel on the windows)

One of the things people say about pixel art is how much detail you can put into it, so you should always try to add that extra bit of work, it's worth it.
I'm going with a simple one though, just a shadow, but it's a bit special.

The roof is the widest part of the hut so the shadow would be the size of the roof, and to calculate the shadow you draw straight lines down from all of the corners of the roof and draw horizontal lines to create a rectangle:

Now you could place your hut on it's shadow and you could say "I'm DONE!"

but to make it a little prettier I made the shadow in an angle (after all the lightsource in my hut isn't straight up)

The light hitting the wall under the roof is something that people might appreciate, I could have also drawn some ivy on the wall, a chimney, etc.

The way the light hits the wall and the floor is geometricaly correct :-) but the process is a bit hard to explain

This is my final hut:

I decided to take out the highlight of the roof top corner line
and now I'm pleased

I hope I helped! now go make your own stuff, pixel architect.