Flanagan, pictured, announced his departure on Tuesday following their third from bottom finish to the Ryman Premier campaign in April.
The former Gillingham, Waterford and Maldon & Tiptree manager succeeded George Borg at the Brentwood Arena at the end of December, guiding the Essex club to four wins, eight draws and 12 defeats as they fought to avoid relegation.
Flanagan, the father of former Blues boss Adam Flanagan, told the Brentwood Gazette that he had hoped to guide the club straight back up next season but understood chairman Brian Hallett's decision to make a change.
Flanagan, who scored more than 100 goals for Charlton Athletic in the Football League, told the paper's website: "I spoke to Brian and he wants to change things around. If Brian wanted me to stay I would have done. I just said to him it's his decision, I will only be disappointed that I couldn't have had a go to get them back up again.
"I've said to Brian I'll still come along and watch games. I haven't fallen out with him at all but obviously he wants to make that change. I don't have a problem with that. It was tough in the Premier Division. My only disappointment is I came in to try to keep the side up. I think people will say it was a struggle, which it was."
He added: "I thought we had an opportunity to stay up but there were games where we should have won which we didn't."
Image courtesy of www.brentwoodgazette.co.uk
Follow us: @rymanleaguenews on Twitter | Ryman League group on Facebook