submission, rejection, rewrite.

My first submission at an American agent got a friendly encouraging rejection today. Apparently the segment "finding a home for your book" is current now, because I found it in the rejection and in a post on the water cooler from forum Mom Jenna herself. I love Jenna, because she is so kind, smart and got chosen last at gym too. I did only one submission, so I can try to submit elsewhere. I find myself experimenting this rather than taking lessons or reading books.
Now I will go to agent query and try again. But the sentence at the bottom of my rejection said I should feel free to submit to the agency again. Does this mean I should rewrite? Or rephrase? Or that my query needs maturation? Or that I chose the wrong type of agent for my query? Or were they just being polite? This and many posts on querying and submitting on the water cooler give rise to many questions. Is there a book on the art of reading rejection forms to submitting writers?
The publisher in Belgium did not reject me yet. But he has my full manuscript and was interested in the subject. Also his press is the ideal audience for my book.