There are 2 types of std's - those which are spread by bodily fluid to bodily fluid and those which spread by skin to skin contact.
Condoms do not protect much against the second kind, since they cover only a portion of the skin. The std u r referring to may be in this category.
Condoms are however highly effective in protecting against those which spread through bodily fluid to fluid contact , including hiv. (though not 100%, since there is always risk of breakage, slippage).
Who said hiv/aids is not an std? It is primarily an std, although it is spread thru blood contact as well. Much like hepatitis c.