A more generic function for point polygon intersects when all that you want are the ID pairs from each intersection. (I am sure that the code could be cleaner or written in a functional style. I am very open to any critiques or improvements, how else am I supposed to learn this stuff....)

point_in_poly.py

import fiona
from shapely.geometry import shape
from rtree import index

def pointInPolyIntersect(pointPath, polyPath, pointIdCol, polyIdCol):
    """
    This function runs intersect operations on a pair of point and polygon data sets.  No
    geometries are returned, just a pair of IDs for each intersection.  The ID columns are
    specified in the args.

    Args: pointPath -  string  Path to input point feature class.
          polyPath -  string  Path to input polygon feature class.
          pointIdCol -  string  Column that holds the ID to be returned from point feature class.
          polyIdCol -  string  Column that holds the ID to be returned from poly feature calss.

    Returns: pntPolyList - list of dictionaries containing a pair of IDs for each
                           point poly intersection {pointID:polyID}
    """

    pointCollect = fiona.open(pointPath,'r')
    polyCollect = fiona.open(polyPath,'r')

    polyDict = {}
    pntPolyList = []

    idx = index.Index()

    idxCounter = 0
    for poly in polyCollect:
        idx.add(idxCounter,shape(poly['geometry']).bounds)
        polyFeat = shape(poly['geometry'])
        polyFeat.polyId = poly['properties'][polyIdCol]
        polyFeat.idx = idxCounter
        polyDict[idxCounter] = polyFeat
        idxCounter += 1

    for pnt in pointCollect:
        pntFeat = shape(pnt['geometry'])
        pntFeat.pntId = pnt['properties'][pointIdCol]
        
        hits = list(idx.intersection((pntFeat.x,pntFeat.y,pntFeat.x,pntFeat.y)))

        if len(hits) == 1:
            pntPolyList.append(dict([(pntFeat.pntId,polyDict[hits[0]].polyId)]))

        elif len(hits) > 1:
            for hitIdx in hits:
                if polyDict[hitIdx].intersects(pntFeat):
                    pntPolyList.append(dict([(pntFeat.pntId,polyDict[hitIdx].polyId)]))

    return pntPolyList