Method 1 -
Reverse the output render's alpha layer when rendering direct from a 3D model (logo)
This is simply a matter of reducing the model's material slot(s) "Transparency-->Alpha" slider to 0.008.
Also reduce both specular sliders to 0 otherwise you may not get full transparency.
If the logo isn't cutting a hole in the background, simply parent (CTL-P) the background plane (child) to the logo (parent) . Use ALT-P to clear the parentage immediately. If there's an outline around the logo, goto the logo's properties and open it's "Display" tab. (down a fair way) and tick the "Transparency" box.
In the render properties (at right) change the shading from Sky to "Transparent"
Output Format -
In the Render properties --> Output tab, set the output format to PNG and select it's RGBA button. (extreme right)
Render the result with OpenGL. (Render menu at top of window)
Method 2 -
This is for when you're starting with an alpha layered image of the logo.
In Blender's 3D window -
Setup the background colour or background image plane.
Add another 2D plane just in front of that. This is for your logo image.
Make the plane's material colour a bright green or one that can be used for Chroma Key.
Set it's transparency-->Alpha slider to 0, and it's specular slider to 0.
Also set the main specular slider to zero or you may not get proper transparency.
In the logo plane's texture properties --> Influence tab, untick the colour box and tick the Alpha box. Make sure the Alpha slider is at full. (1.0) This will force the logo to take on the flat matte colour, namely the green used in it's material slot.
Set up the Compositor as shown and the flat green coloured logo will be converted to transparency.
Render it out as a .png image using --> Blender's Internal render <--- Make sure the "Compositor" box is ticked in the render properties. (post processing tab)
Set the output format as in Method 1 above, including the RGBA button.