Because the book is narrated from Holling Hoodhood's perspective, the tone of the book mirrors his attitude about a lot of things. That means the tone, more often than not, is not overly positive. Holling is upset about a lot of things. His dad is a workaholic that doesn't know how to show any love and support toward his children. His mother is pushover and doesn't stand up to Mr. Hoodhood. Holling is culturally different than everybody else at his school. He is not Jewish, nor is he Catholic. He stands out for this reason, and he believes that he is being punished for it as well by having to spend his Wednesdays with Mrs. Baker.
I would describe the tone of the book as bitter much of the time. Holling isn't angry and hateful, but he doesn't express a lot of joy either. The bitter tone is reinforced by the continuing Vietnam war, Mrs. Baker's missing husband, and the continued distancing of Holling's sister.