sales_flat_order is the full name of the table and so you have to use alias in $installer->getTable()
In $installer->getTable() parameter like module_alias/table_alias.
In that case try with
$installer->getTable('sales/order')
When you write this it will return table name sales_flat_order
because
module_alias = sales
table_alias = order
EDIT
You can use below script to add new column. It works fine in my system
$installer = $this;
$installer->startSetup();
$installer->getConnection()
->addColumn($installer->getTable('sales/order'),'custom_value', array(
'type' => Varien_Db_Ddl_Table::TYPE_TEXT,
'nullable' => false,
'length' => 255,
'after' => null, // column name to insert new column after
'comment' => 'Title'
));
$installer->endSetup();
I am using Varien_Db_Ddl_Table::TYPE_TEXT insted of Varien_Db_Ddl_Table::TYPE_VARCHAR because TYPE_VARCHAR is deprecated
You can check @ Varien_Db_Adapter_Pdo_Mysql::$_ddlColumnTypes
And If you specify type TYPE_TEXT but set length to lets say 255 Magento will create a MySQL column of VARCHAR type.
Best Answer
Take a look at this: https://stackoverflow.com/questions/10074358/how-to-increase-maximum-size-of-csv-field-in-magento-where-is-this-located
Apparently you have to manually change the type of the field but it seems risky. One of the answers claims to have done it without any problems though.
Alternatively, you could try to estimate if your field will really need more space. MySQL type TEXT can fit a bit over 65, 000 characters.