Perhaps you are a little more dehydrated in the morning. Especially if you are one that avoids drinking water before bedtime or spent the previous night drinking stuff that is also a diuretic. Dehydration does tend to increase HR from what I've heard and read in non-authoritative articles and here at BF.

I don't ride in the early morning, I tend to ride midday. But for the few early morning rides I have done, I haven't noticed a difference. However I tend to drink a glass or two of water within a hour or so prior to bed.