You titled this "Rotary Cutting" so I thought your size problem was due to the cutting. But then in your post, you said they weren't the same size after cutting and sewing, so I'm wondering at what stage the size gets inconsistent.
Some beginner tips from another beginner:
1. When you decide what size to cut your pieces, make sure to add the seam allowance on all sides. For example, if you are cutting a strip that you will then cut into squares, and your seam allowance is 1/4 inch, you need to add 1/4 inch to each end of the strip and 1/2" for each cut you'll make into squares (so it's 1/4" for each of the squares).
2. Use the same ruler for all your measurements, because they can differ by 1/16 or 1/8 of an inch, and this adds up.
3. Until you have your sizes under control, only cut one layer of fabric at a time.
4. Hold the ruler down as you cut. It should be over the side of the fabric that is not being cut to size, the side that will be left after you cut your piece.
5. Hold the rotary cutter straight up, so it's perpendicular to the cutting surface. If you're cutting a long piece, move your hand along the top of the ruler as you go, being careful not to move or slide it or the fabric.
4. Cut starting closest to you, moving away from you.
5. When you finish making the cut, you may want to measure it to confirm that it's the right size before going on to your next cut.
6. If it's just slightly off, like 1/8" or less, your seam allowance should cover that flaw.
7. Mark the seam allowances on the wrong side of the fabric so you know exactly where you need to sew. Use a fine point/tip, because a thicker one makes a larger line, which is less precise. You can use a mechanical pencil, a fabric marking pencil in white, yellow or some other color, or washable marker if it doesn't bleed into the fabric.
8. When you sew two pieces together that have pieces within them, don't line them up end to end, but seam to seam. So if you have strips of three squares each and you want to attach the strips to make a nine patch, line up the middle seams and pin, then the outer edges and pin, stretching or leaving loose as needed to make them fit.
Oh, yeah, and what amma said! Press each seam as you go by just setting the iron on it. Don't drag the iron around over it or you'll skew the fabric. (Although it occurs to me that this might be a way to adjust for pieces of different sizes.)