I think putting "This project is used by X, Y and Z" on your website would still constitute trademark infringement. That it's a factual statement is irrelevant. The purpose of trademark laws is to prevent confusion in the marketplace. The pertinent question here is whether the statement creates a false impression that X, Y, and Z are endorsing your product. The answer is a clear yes.

If you write an blog post complaining how X, Y, and Z are using your product but won't let you use their logos, then you'd be in the clear. That's covered by fair use. Identification of the companies in question is absolutely essential to the message you're trying to convey.