They made me sit in the back...
those assholes....

There are actual reasons for this:
1) It allows the animators to get frontal and left side views of the character without having to add in a complicated background full of people.
2) It allows them to look out the window and see plot developments.
3) Since the viewer doesn't see the class not reacting to the characters' antics there is no disruption of the immersion that would occur if the class could be seen. And it allows the characters to complete whatever actions/conversations they are involved with and move the plot forward.

Now that I have thoroughly removed any sort of glamour from this remarkable coincidence, all I can say is... You're Welcome.

Yup, all main characters sit there in Animes.

In Nichijou, the main characters do sit in the back but on the other side of the room, next to the door.

i always get placed in the middle.

That's also where I always sat...

So Hitome is the main character of Madoka?

Another....Yuru Yuri...in Toradora they dont...those are the only ones i can remember

Maybe it's just easier to draw? If there in the middle of the room they'd have to do all the other desks/pupils Ect. Or the other side they'd have to do educational displays on the wall or something? Seeing as for a window all they have to do is do the sky or white it out like seen? I dunno Just a theroy

Actually, Yugi Mutou moves places a lot between different seasons and manga arcs. Probably to keep up with the fact that he changes school year.
Pretty sure Yoh Asakura doesn't sit by the window either.
Or Naruto (yes, they have classrooms)
Or Lelouche vi Brittania.
Or Ciel Phantomhive.
Or Kaoru, Hikaru or Haruhi from Ouran.

Me realizing Clannad he sits there.