Absolutely! Power supplies are designed to cater for many different power
configurations, hence there are usually a few stray connectors after
installation.
The only time this is a problem is if you have forgotten to plug something in,
so double check that you do not have any empty power sockets on the
motherboard, graphics card etc...
...and while you're in there use a couple of cable ties to tie up the spare
connectors somewhere safe. We don't want them finding their way into the CPU
cooler now do we ;-)