I agree. I used to put a Weber Cover on my Q100 on the deck, but every time I took it off, there was moisture under it, between the hood and the lid. It was not a worn out cover either. It just held in and condensed the moisture with the grill getting hot and cold as the sun heated up in the day time and it cooled in the evenings. Every day, more moisture condensing under the cover is not a good thing for a grill. I now simply put a large tote over the grill. Looks stupid, but keeps the rain out and allows it to breath all day/night. The CI grates on those Q grills will be happier for sure.
The covers are great if they are well vented, but where ever they lay flat against a surface, you are likely to have a problem. The newer covers don't have the venting on them like the older ones did.