No one knows (or at least they can't agree) on what causes lingering Lyme symptoms after treatment. One camp of doctors do believe in persistent infection, but that is sadly the minority. The majority medical opinion is that some "post-Lyme" syndrome, possible autoimmune in nature, is why some people still have symptoms after the standard treatment with antibiotics.
Since the situation is so poorly understood, it's tough as a patient to decide what to do over issues like vaccination. As with any choice in life, I think it's good to consider the risks versus the benefits. Last year, I was much more sick with Lyme than I am this year. I was also in a situation where I was only around a few people between work and home. So I felt that my risk of contracting h1n1 was relatively low while the risk of adverse affects from the vaccine, given my more fragile health, was relatively high. I skipped the vaccine.
This year I'm reconsidering, as my health has improved and I'm in a new job that places me in contact with way more people.
I'd suggest weighing your options and also to ask you doctor about what to do, then if you can, ask another doctor or try to get a second medical opinion.
Good luck, and hopefully we all stay flu-free this year!
Greetings.
Your MD treated you according to what sounds like the mainstream medicine approach for Lyme: a couple weeks of antibiotics and you're good to go, no matter how you feel.
Many of us never have a rash either, so that's not determinative of illness or its absence.
I don't know about the flu vaccine, but I would suggest strongly that you find an MD who follows the more advanced standards in treating Lyme as published by the International Lyme and Associated Diseases Society (website: ILADS.org). If you need help finding a so-called LLMD ('Lyme Literate MD'), let us know.
Perhaps someone else here has been told one way or the other about the flu vaccine.
Take care!