You need to put the new version in the 'tag' folder of your repository. The folder name should be the same as the version number inside the readme file. Make sure that the version number has the same number of digits, as they are sorted numerically. Version 1.1 is 'lower than version 1.15, because the version number doesn't have the same number of decimals. I always label my versions 1.10, 1.11, 1.20, 1.21, etc.
If you have synced the repository correctly, you should get an email back from WP that the new version is available. Can take up to an hour.
I always put the latest version in the root of the repository, and in the 'trunk' folder of the repository, and then in the new version number folder in the 'tag' folder. Maybe redundant, but works for me.
-- (root) (latest version here)
|--- trunk (latest version here)
| --- tag
\--- 1.00 (prior version)
\--- 1.01 (latest version here)
If you do all that, then all users of your plugin will see the upgrade notice. Not right away (patience, grasshopper), but probably within an hour.