Here is a script that will randomly scale between two values the trees that are painted on the terrain.

To set this up :

Create a new javascript named ScaleExistingTrees. Use the code below.

Attach the script to the terrain object.

Drag and drop your terrain into the the Inspector.

Set the min and max scale to your liking.

How to use this :

Right-click on the script component in the Inspector, then a drop-down selection box appears. Example :

Click on Scale Existing Trees, now your trees have been scaled =]

Remove the script from the terrain when you are done.

ScaleExistingTrees.js

 #pragma strict
 
 public var terrain : Terrain;
 
 public var minScale : float = 0.8;
 public var maxScale : float = 1.2;
 
 #if UNITY_EDITOR
 @ContextMenu( "Scale Existing Trees" )
 function ScaleExistingTrees() 
 {
     // check if there is no terrain in the inspector, then use the current active terrain
     if ( !terrain )
     {
         terrain = Terrain.activeTerrain;
     }
     
     // check if maxScale is less than minScale
     if ( maxScale < minScale )
         maxScale = minScale;
     
     // variable for storing random calculated scale
     var rndScale : float;
     
     // store reference of all the current trees
     var treeInstances : TreeInstance[] = terrain.terrainData.treeInstances;
     
     // cycle through each tree
     for ( var t : int = 0; t < treeInstances.length; t ++ )
     {
         // calculate random scale
         rndScale = Random.Range( minScale, maxScale );
         
         // apply to curent tree in array
         treeInstances[t].heightScale = rndScale;
         treeInstances[t].widthScale = rndScale;
     }
     
     // apply treeInstances back to terrain data
     terrain.terrainData.treeInstances = treeInstances;
     
     Debug.Log( "Scaling Trees Complete" );
 }
 #endif

if your tree is procedural, and you don't wan't to deal with scripting, check this out. http://forum.unity3d.com/threads/unity-tree-scaling-inside-terrain-no-effect.98774/