Probably...

 

However in a Campaign they may not...

 

Or they do and there are 2 routes

CnC route:  Plot changes depending on what side you play

Warcraft route:  you play one faction, then another in a specific order giving it a larger plot. 

That one makes better sdense for Halo... but it may mean you go the Cov first...
 

I have a feeling they will be...with Halo 2 giving us the Arbitar for half the game, and that much insight into the Covie's intent/fighting style, it seem a little awkward to just be blowing their brains out the entire time. 

Apollyon:

Will the Covenant be a playable faction in this game? I hope they will, as I enjoy taking advantages of both sides.

Under the FAQ's of Esembles official website for Halo Wars they say "Stay Tuned" when asked if the covenant can be playable.  I bet we will learn more at E3.

or whatever E3 was replaced with now...E33 or whatever its called. 

I think it would be stupid for the Covenant not to be playable in Halo Wars.

 Maybe they can make it like you have to beat the game playing as the Humans/UNSC and than you can play as the Covenant. I think that'd be a pretty nice setup.
 

In the faq it says you can play as human, and we'll see about about covenant, but what about about flood? The game needs more than 1 or 2 factions. Especially in multiplayer, isnt that what Halo is all about.

this has been discussed already here

simpley no, 'Halo wars' takes place before the events of halo 1.

The_Jim:

In the faq it says you can play as human, and we'll see about about covenant, but what about about flood? The game needs more than 1 or 2 factions. Especially in multiplayer, isnt that what Halo is all about.

This has been talked about.  To answer your question though, Esemble Studios has not released any additional information besides what has been at the X06 Keynote.  Nothing confirmed yet.

You guys are going to need this:

 

if u can play as flood, then it would pwn, u could like convert dead humans or cov into flood :D, like monks in aoe 2

that would pwn hard

 

HE11 NO!!!! The flood should g die in a huge fire... no one wants to fight them and no one wants to play them i would say

SheeAIDS:

if u can play as flood, then it would pwn, u could like convert dead humans or cov into flood :D, kanda like monks in aoe 2

that would pwn hard

 

Nope this games set before the fall of reach yet alone the discoveries of the halo installations from where the flood came from.

lol, i compleatly forgot tat the flood appear in halo 1 , this is before halo 1 , srry :D

For the 100th time, the flood won't be in the game because Halo Wars is taking place before Halo:Combat Evolved.