You probably have an alias somewhere, mapping 
cp to 
cp -i; because with the default settings, 
cp won't ask to overwrite. Check your 
.bashrc, your 
.profile etc.
See cp manpage: Only when -i parameter is specified will cp actually prompt before overwriting.
You can check this via the 
alias command:
$ alias
alias cp='cp -i'
alias diff='diff -u'
....
To undefine the alias, use:
$ unalias cp