TikZ: Why is "dimension too large"?

Use x=0.010cm, y=0.10cm instead of xscale=0.010, yscale=0.10. The scale is only applied after the coordinate has been transformed into pt already and that is where you exceed \maxdimen.

\documentclass{article}
\usepackage{tikz}
\begin{document}
\begin{tikzpicture}[scale=1.0, x=0.010cm, y=0.10cm]  
\draw[magenta,line width=1pt] plot coordinates {  
(1,100.00) (2,99.29) (3,99.14) (4,98.65) (5,99.31)  
(6,99.30) (7,99.70) (8,99.98) (9,98.88) (10,99.77)  
(11,99.75) (12,99.88) (13,99.55) (14,100.15) (15,100.21)  
%...  
(561,154.35) (562,154.60) (563,154.38) (564,156.64) (565,156.26)  
(566,157.17) (567,157.78) (568,157.11) (569,154.20) (570,154.05)  
(571,153.74) (572,154.54) (573,153.87) (574,154.95) (575,154.00)  
(576,153.82) (577,154.67) (578,155.36) (579,155.63) (580,152.95)  
};  
\end{tikzpicture}
\end{document}