From mboxrd@z Thu Jan  1 00:00:00 1970
From: Jambunathan K <kjambunathan@gmail.com>
Subject: Re: hiding footnotes
Date: Wed, 28 Nov 2012 22:56:50 +0530
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> Reading an org-file. I should note, it is the highlighting that is the
> problem, not the footnote itself. If I could somehow toggle it to the
> color of the text, that would solve my problem.

Put your cursor on the footnote.  Then do

    C-u C-x =

In the resulting buffer, toward the end, you will see something like
this.

    ,----
    | There are text properties here:
    |   face                 org-footnote
    |   font-lock-fontified  t
    |   font-lock-multiline  t
    |   fontified            t
    |   help-echo            "Footnote reference"
    |   keymap               [Show]
    |   mouse-face           highlight
    |   org-category         "test-new"
    |   org-no-flyspell      t
    `----

Click on the face property (which is `org-footnote').  Click on
"customize this face" link.  Change the face foreground color to
whatever you want.

Or 

A fast way to do that would be 
    M-x customize-face RET org-footnote RET

You can also try
    M-x customize-group RET org-faces RET
--