Is this probably why Mike explicitly said to the crew not to talk or bother Walt and Jesse in any way.
It's certainly a possibility but if I was to make a conclusion I'd probably lean towards saying no; the primary reasons being that Todd was used in the train robber and the announcement was to the entire crew.
Now, this isn't to say that Todd may not have been the primary focus, but if I was to interpret Mike's stern warning it would be a stern reminder of their position; that is, those who set up the house, nothing else. Walter and Jesse, to them, are not colleagues, they're not friends, they're not potential partners, and they are certainly not targets (as the crew had been involved in small time robbery). More than anything, Mike wanted their operation to be contained (particularly with the DEA presence) and, under no circumstances, wanted news of their operation to spread, a further problem to deal with (a disrespectful employee flying too close to the sun), or a 'potential Walter' (somebody who would want more than what they were being paid or try to operate a solo venture). Perhaps others took it differently, but I pretty much left his warning just so they were reminded of their position and would not interfere with the business that was being conducted inside of the houses.
Again though, it could definitely be interpretted how you've implied it but I imagine all of the crew had some connections (some clearly more than others though) to criminal activity (since they were all petty thieves beforehand) and wouldn't personally think he was specifically thinking of Todd in his warning.
Good luck... Couldn't bring myself to finish that season. S1 was great though...
It's a change of pace and I know many don't like it on their first watch but I would highly advise finishing it. It's a very slow pace overall (it is definitely my second favourite seasons of The Wire though and it has, by far, my favourite sequence in film or TV show at the end of the season) but everything comes together magnificently well by the end. The season plays an absolutely crucial role in the entire show as it firmly cements that the show is not merely a 'cops and robbers' style show and it has higher aspirations, that's in addition to the major role it plays for the remainder of the series. What I would strongly advise is for you to finish the second seasoon and, after that, finish the remainder of the show and, once you've done so, rewatch it (maybe not immediatey, but gradually, maybe in a two episode block every week or two) as I know for many who have watched the show in my vicinity have shared your lack of enthusiasm for it but, upon a rewatch, have drastically increased their admiration for the season. Of course, it's not for everyone so it's certainly possible you won't improve your opinion but I would implore you to at least finish the season (and if it's been awhile to rewatch the episodes you've already seen in the season because there are so many plot threads you absolutely do not want to forget some and be left somewhat bewildered at specific events).
