For anyone who stumbles across this post in the future as I have.
Coming from a recruitment background it has been my experience that any candidate or agency who attempts to bypass recruitment and go straight to the hiring manager will be looked upon in a negative light (with many agencies being basically being put on a do not use list for continuously doing this).
Hiring Managers often bring recruiters candidates who they would like to hire because they're a friend of a friend or an old work colleague and unfortunately it is rare that these people are the right fit for the role or company. Due to this, recruiters are often very sceptical of any candidate who has not bothered to come through the correct channels.
You may have been rejected in the earlier stages of the recruitment process by HR / Recruitment because the role requires a specific amount of experience in years etc. Perhaps there have been other candidates who have the skills and experience to match yours but can also offer other skills or expertise that would complement the role and the team.
Or perhaps in the case of BryanH you may have spoken to the company in a similar style to his second response and come off as rude, condescending and even slightly up yourself. It’s never nice to refer to someone as a ‘drone’ simply because you were not hired or had a bad experience. HR people work very hard to get the right person for the right role and that job is often made a lot harder because of people with that kind of attitude. Most hiring managers do not appreciated being contacted directly by candidates (especially those who have already been rejected) as they tend not to go away once they get a name and a number.
If you receive what is likely to be an automatic reply (as it sounds like OPs response was) then there is no reason to email back unless you would like more information or feedback regarding why you weren’t successful (but keep in mind the reply may come from an unmonitored system). If you have already been through part of the recruitment process such as interviews and receive a phone call or a direct email from the recruiter then once again it is fine to query what could have been done to improve your application or interview techniques and perhaps even thank the recruiter for their time (as OP was looking to do).
It is not always looked upon as spam and honestly when you get a lot of angry and bitter rejected candidates (who proceed to call the hiring managers or anyone in the company and keep pushing their applications or those who send back something like your loss) those who are actually polite, professional and respectful do tend to stay in a recruiters mind when other roles open up as those are the kind of employees companies are generally looking for, not someone who is going to insult staff members and fail to follow proper procedures (because if you are not willing to follow the process to get a role, then how do we know you would follow processes and procedures within the role?)