The Evangeleon units are MASSIVE compared to Gundams. The Gundam Wing Zero is about 17 meters tall. The EVA 001 is somewhere between 40 to 200 meters tall. In other words, the Gundam compared to the Evangeleon is probably around the same size as a human is to a Gundam.
Now, granted, for the most part in the anime the Evangeleons are slow, clumsy, clunky and overall not particularly impressive in terms of maneuverability. In most of the battles they basically just dragged out a giant gun and did one shot. Moreover, once unplugged-- they are only operational for about 3 minutes. So maybe the Gundam can avoid being swatted or stomped for long enough for the unit to run out of power-- but otherwise… its not exactly a threat.