Actually there's nothing about resources in particular that prevents you from using it multiple times. A perfect example of this is brush resources, style resources, etc. You define them in XAML and the XAML parser creates a single instance of the resources and stores them in the resource dictionary and these brushes, styles, etc can be used as property values many times even though only a single instance of the resource was created.
But having said that, as you noted, you can't really define a Rectangle resource and use it multiple times in the visual tree. This has nothing to do with the fact that it's a resource, but rather it has to do with the fact that a FrameworkElement cannot be a child of more than one parent element.
So what we have instead is called "templates". These tell WPF how to create an element tree but does not actually create the tree until you instantiate the template. Below is an example.
<UserControl>
<ItemsControl ItemsSource="{Binding WholeBunchOfItems}">
<ItemsControl.ItemTemplate>
<DataTemplate>
<Grid>
<Rectangle Fill="Yellow" />
<ContentPresenter Content="{Binding}" />
</Grid>
</DataTemplate>
</ItemsControl.ItemTemplate>
</ItemsControl>
</UserControl>
In this example I've bound an ItemsControl to a collection of some sort. For each item in the collection, the ItemsControl will use my DataTemplate to render the item. Within a DataTemplate you can use data binding to access the current item.
I would suggest reading up on MSDN about ControlTemplate, DataTemplate, and Style. These are all important concepts in WPF/Silverlight.