I have a 98Honda Accord and the alternator has been rebuilt twice and the battery is brand new.
Its still not charging as it should be.
What can it be?

Corroded firewall connection.

Did you buy a rebuilt alternator or take it out and have someone rebuild it for you?

If you purchased a rebuilt assembly, where did you buy it from? While I use NAPA for some parts, I won't sell my customers any of their alternators because the rebuild-quality is definitely lacking.

The Powertrain Control Module (PCM) controls the charging system on your vehicle.
Have you tested the PCM?
Have you verified battery power to the alternator and solid ground circuits?

I enjoy rebuilding alternators. Here's the approach I follow:

https://www.askmehelpdesk.com/cars-trucks/faq-how-troubleshoot-repair-maintain-hondas-selected-other-vehicles-46563-6.html#post666293

CaptainRich is correct that the ECM controls the voltage regulator on most modern-day vehicles. Usually, however, the problem is with the alternator, not the ECM. I suspect the brushes are too short or the slip rings weren't cleaned properly. It all depends on the quality of the parts and workmanship. Usually, the real problem is something pretty basic. It could certainly be a bad voltage regulator or bad diodes, but that's less likely. Ensure all connections from the alternator to the battery are clean--apply dielectric grease. Check the mega fuse connections between the alternator and the battery, too, after disconnecting the negative battery terminal.

Most auto parts stores will test alternators for free.