The short rule is, it's almost always OK to boo your own team.
If you feel the need to motivate your team to help them along and you have arrived at the point where you think a hearty boo or heckle is what's going to do the job, then you do it. You boo, Boo Bird. You boo to your hearts content and then maybe even do one of those tennis whistles or a belly-itcher chant. This is your right as a paying fan. You do it.
Indeed, some psychologists believe that being hostile to a batter may positively affect that batter's performance.