Intonation is something that every upright player that I've ever spoken with (whether they're weekend warriors, touring jazz players, or working in a symphony) still works on. If you continue to put in the work required, it WILL improve. I didn't even start playing upright until I was working on my undergraduate in jazz performance, and for the first few years, my intonation was horrible. But, it gradually got better, and as it got better, my confidence in my intonation grew (which I believe is a big part of playing in tune).
A few things that really helped me:
- Use drones on more than just scales and arpeggios. Use them on your classical etudes, practice jazz solos and melodies to them, etc... Play slow enough to be able to correct your intonation, without "sliding" into notes
- Practice shifts from one position to the other (both single-string and across strings) with the drone
- walk basslines against a drone (example: put your drone on F, walk an F blues)
- walk along with recordings
- in general, play along with something that has steady pitch, whether that is a drone, recording, or another musician (playing with pianists and guitarists is great)
Good luck. Like I said above, don't get discouraged - it WILL get better with practice.