This is some example code I wrote the for the MSDN forums to showcase how you can programmatically set permissions. This code will work for splists or spwebs (in the example it’s SPList permissions, but just changing those calls to go off of Web will switch it). In addition, this shows how to set permissions automatically at feature activation using a SPFeatureReceiver. Double bonus! 
// actions to perform when feature is activated/removed
class FeatureReceiver : SPFeatureReceiver
{
#region Activate and install feature
public override void FeatureActivated(SPFeatureReceiverProperties properties)
{
SPWeb web = (SPWeb)properties.Feature.Parent;
SPList list = web.Lists["ListName"];
//get users and groups so we can add them to the list
SPUserCollection users = web.Users;
SPGroupCollection groups = web.Groups;
//get current permissions and permission definitions so we can apply permissions
SPRoleAssignmentCollection rolesCol = list.RoleAssignments;
SPRoleDefinitionCollection roleDefs = web.RoleDefinitions;
//get a specific user or ad security group by username
SPUser myUser = web.EnsureUser(@”DOMAIN\MySecurityGroup”);
SPRoleAssignment addUser = new SPRoleAssignment(myUser);
//create new roles binding for user or group
SPRoleDefinitionBindingCollection bindUser = addUser.RoleDefinitionBindings;
//give contribute rights to user or group, this can be the friendly name of any role definition
bindUser.Add(roleDefs["Contribute"]);
//add the user to the existing role assignment collection for the object 
rolesCol.Add(addUser);
//and finally we update to apply our changes
list.Update();
}
}
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