You need to edit skin1/modules/Product_Options/customer_options.tpl and comment out the code similar to this
Code:
{if $v.is_modifier eq 'Y' && $o.price_modifier ne 0}
(
{if $o.modifier_type ne '%'}
{include file="currency.tpl" value=$o.price_modifier display_sign=1 plain_text_message=1}
{else}
{$o.price_modifier}%
{/if}
)
{/if}