Square roots not on same height

You're not doing anything wrong, you're just wanting something that is not the default. The reason for the different \sqrts is because \rho and b (and l) have different height and depth, which \sqrt accommodates.

Here are some alternatives (non-exhaustive) that tried to show you what is possible:

\documentclass{article}
\usepackage{mathtools}% http://ctan.org/pkg/mathtools
\begin{document}
\begin{flalign*}
  T &= C\frac{1}{\sqrt{G}}\sqrt{\rho}\sqrt{b}\sqrt{l} \\
  T &= C\frac{1}{\sqrt{G}}\sqrt{\vphantom{b}\rho}\sqrt{b}\sqrt{l} \\
  T &= C\frac{1}{\sqrt{G}}\sqrt{\mathrlap{\smash{\mkern-2mu\rho}}\phantom{b}}\sqrt{b}\sqrt{l} \\
  T &= C\frac{1}{\sqrt{G}}\sqrt{\vphantom{b}\mkern-2mu\rho\mkern2mu}\sqrt{b}\sqrt{l} \\
  T &= C\frac{1}{\sqrt{G}}\sqrt{\rho b l} \\
  T &= C\frac{1}{\sqrt{G}}\sqrt{\rho\,b\,l} \\
  T &= C\frac{1}{\sqrt{G}}\sqrt{\mkern-2mu\rho\,b\,l}
\end{flalign*}
\end{document}

Options include

• horizontal adjustment of \rho using \mkern (math kerning);
• removal of depth (and height) using \smash;
• vertical struts using \vphantom;
• overlapping (math right overlap) with \phantom content to provide similar horizontal spacing/placement.

Many other options also exist, including moving \sqrt{rho} to form part of the \frac.

Don't use flalign for left aligning displays; this is a job for the fleqn option.

The problem is that a lonely \sqrt{\rho} shouldn't have too much space between the bar and the rho, but this obviously gives asymmetric results when square roots appear together like in

$\sqrt{a}+\sqrt{b}$

There are several tricks for equalizing square root symbols, each with its pros and its cons.

A couple of adjustments are to be made anyway: the \rho under the square root should be backspaced a little, to avoid a hole; between two consecutive square roots a thin space should be added.

In order to solve the main problem, two strategies are possible: the first one is easier, as it consists in adding \mathstrut under the square roots; the second strategy is to remove the depth from \rho and adding a phantom b.

Which one to choose depends on many factors; leave these decisions to the final revision of your document. A change in notation might make obsolete one of these constructions.

\documentclass[fleqn]{article}
\usepackage{amsmath}
\usepackage{lipsum} % just for the example
\begin{document}
\lipsum*[2]
\[
T=C\frac{1}{\sqrt{G}}\sqrt{\!\rho\mathstrut}\,\sqrt{b\mathstrut}\,\sqrt{l\mathstrut}
\]
\lipsum*[2]
\[
T=C\frac{1}{\sqrt{G}}
  \vphantom{\rho}\sqrt{\!\smash[b]{\rho}\vphantom{b}}\,\sqrt{b}\,\sqrt{l}
\]
\lipsum*[2]
\end{document}