I haven't yet encountered any rain, but when assembling mine I noted the same thing. Ran over to a "Dollar Store", plunked down $1 for some Velcro bits, and attached to the bottom corners and center of the window and its flap.
Once it heats up here this summer I may need to do some minor stitching to keep the Velcro from peeling off, or maybe upgrade to some snaps, but for now (cool weather) it seems to work fine.