It really depends on the time of day and where you park. If you have a van or SUV I'd avoid parking with luggage in my car. If you can lock all your luggage in the trunk you should be ok.
There is a parking lot directly across from the restaurant near the trailhead of Manoa Falls park. I would feel safe parking there during lunchtime. Btw, don't eat at the restaurant - it's horrible.
The parking area near the start of the trail of Makapuu is also very heavily trafficked and I would be less worried there. I've done this hike several times and I've never been alone on the trail. I definitely wouldn't park on the side of the road or near the start of the road the turns into the parking lot.