I am having the same problem. "Some of my subscribers are saying that the new post notification emails received (generated by S2) are going into their spam folder."
My clients are also saying their recipients are not getting the notifications send by Subscribe2. I had one client provide evidence today that all the subscribed users in the office, that the notices do in fact go the Junk folder. After a little research, I have found that users of Outlook and Gmail as examples, have over time repeatedly marked the Subscribe2 notifications as spam, therefore currently the default setting on these systems junk filters is to identify Subscribe2 notifications as spam. This is a grave problem, essentially rendering the Subscribe2 provision as ineffective and defective.
One cannot expect every recipient of a notification to fish out the spam and train the filter as a solution? While this is one method, the majority of users never pay any heed to the Junk folder, and therefore much of the Subscribe2 notifications are never seen or read. What is needed is the revised construct of the default email templates content, that they be altered significantly as not to trigger these spam filters. While the Subscribe2 WordPress user could alter the default email, it has become a universal plugin issue and should be adjusted to assure the value of the product.
I cannot provide Subscribe2 to my clients, i.e. as a potential purchasing customer of the HTML version or WPMQ, when a problem of this significant nature exists, fully negating its purpose. E.g., notifications are being universally treated as spam, end up in the recipients Junk where most do not see them.