I have already read a few pages such as this one subset GRanges

library(GenomicRanges)
library(GenomicFeatures)
#make the list of chromosomes to filter by

#make the database and transcripts
txdb <- makeTxDbFromGFF("Me/inputs/gencode.v19.chr_patch_hapl_scaff.annotation.gtf", format="gtf")
tscripts <- transcriptsBy(txdb, by="gene")

> #test the subsetting.. seems to work
> tscripts@unlistData@seqnames@values[tscripts@unlistData@seqnames@values == "chr1"]
   [1] chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1
  [34] chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1
  [67] chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1
[100] chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1

But it doesnt work as expected..

> tscripts[tscripts@unlistData@seqnames@values == "chr1"]
GRangesList object of length 5272:
$ENSG00000000419.8
GRanges object with 7 ranges and 2 metadata columns:
      seqnames               ranges strand |     tx_id           tx_name
         <Rle>            <IRanges>  <Rle> | <integer>       <character>
  [1]    chr20 [49551404, 49575087]      - |    182563 ENST00000371588.5
  [2]    chr20 [49551404, 49575087]      - |    182564 ENST00000466152.1
  [3]    chr20 [49551404, 49575092]      - |    182565 ENST00000371582.4
  [4]    chr20 [49551433, 49562398]      - |    182566 ENST00000494752.1
  [5]    chr20 [49551482, 49575058]      - |    182567 ENST00000371584.4
  [6]    chr20 [49551490, 49575069]      - |    182568 ENST00000371583.5
  [7]    chr20 [49552685, 49575069]      - |    182569 ENST00000413082.1

I also tried this, but got empty elements

> tscripts[seqnames(tscripts) == "chr1"]
GRangesList object of length 63568:
$ENSG00000000003.10
GRanges object with 0 ranges and 2 metadata columns:
   seqnames    ranges strand |     tx_id     tx_name
      <Rle> <IRanges>  <Rle> | <integer> <character>

$ENSG00000000005.5
GRanges object with 0 ranges and 2 metadata columns:
     seqnames ranges strand | tx_id tx_name

$ENSG00000000419.8
GRanges object with 0 ranges and 2 metadata columns:
     seqnames ranges strand | tx_id tx_name

What am I doing wrong here?

First, please avoid accessing the slots of the object, as they are an internal implementation detail. Code accessing the slots will be cryptic and fragile.

Note that this object is not a GRanges but a GRangesList. You might want to simplify to a GRanges using something like:

tscripts_gr <- stack(tscripts, "gene_id")

It depends on what you want to do downstream. Some more details would help.