How can I return a value from a CakePHP list array to use in a form?

There are a few oddities in the code in the question:

Conditions

'conditions' => array('School.active' => !null)

!null is simply true, this is identical to using:

'conditions' => array('School.active' => true)

If you want to check for not-null the condition to use is:

'conditions' => array('School.active NOT' => null)

OR

'conditions' => array('NOT' => ('School.active' => null))

Options

'options' => array($schools)

$schools is already an array - this is creating a nested array, which will be interpreted as a select with an optGroup named "0". I.e. like this:

<select name="data[User][school_id]" id="UserSchoolId">
    <optgroup label="0">
        <option value="2">School A</option>
        <option value="3">School B</option>
        <option value="1">School C</option>
        <option value="6">School D</option>
    </optgroup>
</select>

It's always a select

You haven't explicitly said so, but whether the user is an admin or not, the input is a select. It sounds like you're expecting a disabled text input, always look at the html source to verify what exactly you're looking at.

This occurs because CakePHP will automatically convert a field named schools_id to a select if there is a view variable named schools. This is also the reason why the first school is always selected irrespective of the auth'ed user's school, the code in the question is effectively:

echo $this->Form->input(
    'school_id',
    array(
        'label' => 'School *',
        'options' => $schools, // implicit
        'value' => $schools[AuthComponent::user('school_id')],
        'disabled' => 'disabled'
    )
);

The result is markup like this:

<select name="data[User][school_id]" value="School C" id="UserSchoolId">
    <option value="2">School A</option>
    <option value="3">School B</option>
    <option value="1">School C</option>
    <option value="6">School D</option>
</select>

There is no school with that value - so the html will act like it's not there and pick the first one.

Solution

You'll need code equivalent to this:

$options = ['label' => 'School *'];
if (!AuthComponent::user('admin')) {
    $options += [
        'value' => AuthComponent::user('school_id'),
        'disabled' => 'disabled'
    ];
}
echo $this->Form->input('school_id', $options);

Obviously, do not rely on the form for security of any kind - a disabled input does not prevent a user editing the html, enabling it and changing the value. Either use the security component (which prevents form tampering), forcefully ensure that the school_id (and any other fields that are relevant) match the auth'ed user's data in the controller action before saving/changing records or both.