Singleton model for modifying future .chart elements
I think you are overdoing the underscores, you will find that conflicts will be rare.

Furthermore, I can understand that you want to centralize the iteration over the chart elements, but why would you want to do that recursively, it does not make much sense to me. 

If you drop underscores and opt out of recursive iteration, your iterator becomes simpler:

  //Applies the supplied function for each chart element in the collection.
  var applyFunction = function ( f )
  {
    $charts.each(function (){ f($(this)); });
  };


This could be converted to a for loop as per your comment

  //Applies the supplied function for each chart element in the collection.
  var applyFunction = function ( f )
  {
    for( var i = 0, length = $charts.length; i &lt; length ; i++ ){
      f( $charts[i] );
    }
  };


Then, colorArgumentButtons becomes simpler as well:

  // Colors all argument buttons.
  my.colorArgumentButtons = function (color)
  {
    applyFunction( function( $chart )
    {
      $chart.find('button').css('background-color', color);
    });
  };


You will notice that I reduced the comments to a one line comment. When you have almost as much lines of comment as code, then you are doing it wrong.

A minor side note on 

selector = typeof selector !== 'undefined' ? selector : settings.chartSelector;


this could simply be 

selector = selector || settings.chartSelector;


All in all, I refactored the code into this ( untested ):

var SuperHappy = (function (parent, $) {

  var my = parent.Chart = parent.Chart || {},
      // default settings
      settings = {
        autoFind: true,
        chartSelector: '.chart'
      },
      // jQuery vars
      $charts = $();

  //Applies the supplied function for each chart element in the collection.
  var applyFunction = function ( f )
  {
    $charts.each(function (){ func($(this)); });
  };

  my.init = function (options) 
  {
    settings = $.extend(settings, options);
    if (settings.autoFind) {
      my.findCharts();
    }
  };

  /// Colors all argument buttons.
  my.colorArgumentButtons = function (color)
  {
    applyFunction( function( $chart )
    {
      $chart.find('button').css('background-color', color);
    });
  };

  // Finds all chart elements.
  my.findCharts = function (selector)
  {
    selector = selector || settings.chartSelector;
    $charts = $(selector);
  };

  return parent;

})(SuperHappy || {}, jQuery);

jQuery(document).ready(function ($) {
    SuperHappy.Chart.init();
    SuperHappy.Chart.colorArgumentButtons('#f00');
});