The 18-55 is at f/5.6 at the long end. Not coincidentally, f/5.6 is the smallest aperture that Canon's AF system (except the top of the line models which keep going until f/8) will actually work at - officially, it simply quits trying if the lens is f/6.3 or darker. Some superzoom f/3.5-f/6.3 lenses cheat, and lie, and say that they are f/5.6 to keep the AF trying. In short, the AF does not have an easy time of it at f/5.6, and the 1000d is a low-end camera with a not particularly brilliant AF system.

A lens with a larger aperture, like a 17-50 f/2.8 style zoom, would give more reliable autofocus. A camera body with a more fancy autofocus system would have an easier time of it with the 18-55. As it is, you must simply deal with it by either supplying more light in the form of an external flash which will project a grid-pattern onto the subject to give the AF something to bite on (this only works at close range, obviously), or do your best to point the autofocus at something that is distinctive and has good contrast against the background.