1) If you want to hide shipping Method Block from Cart page you can edit checkout.xml layout file, you can find that file in frontend/your_package/your_theme/layout/checkout.xml, then look for the
<checkout_cart_index translate="label">
tag and remove or comment the following line within reference name content
<block type="checkout/cart_shipping" name="checkout.cart.shipping" as="shipping" template="checkout/cart/shipping.phtml"/>
2) You can hide specific shipping method on magento cart by editing cart's shipping.phtml. It's located in frontend/your_package/your_theme/template/checkout/cart/shipping.phtml
Find the following lines:
<?php if (($_shippingRateGroups = $this->getEstimateRates())): ?>
<form id="co-shipping-method-form" action="<?php echo $this->getUrl('checkout/cart/estimateUpdatePost') ?>" class="co-shipping-method-form">
<dl class="sp-methods">
<?php foreach ($_shippingRateGroups as $code => $_rates): ?>
and add some code after the second foreach to skip shipping method you want
<?php if ($code == 'your_shipping_method_code') continue; ?>
p.s. If files located in base package default theme, make sure to copy that file to your package theme first.