I find my longarm prefers cotton thread. I generally use cotton thread for piecing too, but found some Gutermann poly that needs to be used, so I am piecing with that. Some of the charities that accept quilts for children in hospitals ask that you use everything cotton in the quilts being sent to them. The reason is that the quilts will be washed in commercial washers and dryers and the poly melts in the high heat used. We all find our favorites and no one way is right or wrong, just what we come to prefer.

I love cotton thread, use it for piecing and quilting, I mainly do FMQ. I just prefer the feel, I use cotton thread & batting, I like having 100% cotton in my quilts.

OMG, I was making one of the jelly roll rugs last week and using a polyester thread on piecing the strips together.
Used my Clover "stick" iron......then I noticed seams were not sewn....so I thought I ran out of bobbin thread...Not
the clover iron melted the thread into oblivion. Yep, learn something new everyday. I'm sticking with cotton, since I use my iron a lot in piecing.

I have used Bottom Line - which is a Superior Threads polyester - almost exclusively for piecing for the last 4-5 years, and not once have I ever had an issue with it melting. I'd be curious to know what brand you were using and what temperature your iron was at, Lady Diana. Of course, without an infrared thermometer, it would be pretty difficult to find out what temp your clover iron was at, I suppose. :(

So do it and totally agree with you.